symmetric_docking

Bindings for protocols::symmetric_docking namespace

class pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockBaseProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol

C++: protocols::symmetric_docking::SymDockBaseProtocol::operator=(const class protocols::symmetric_docking::SymDockBaseProtocol &) –> class protocols::symmetric_docking::SymDockBaseProtocol &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

get_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::symmetric_docking::SymDockBaseProtocol::get_highres_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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_lowres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::symmetric_docking::SymDockBaseProtocol::get_lowres_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockBaseProtocol) str

C++: protocols::symmetric_docking::SymDockBaseProtocol::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

set_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.symmetric_docking.SymDockProtocol

Bases: pyrosetta.rosetta.protocols.moves.Mover

Main Symmetric Docking protocol class

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

Mover Methods /////////

C++: protocols::symmetric_docking::SymDockProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol

C++: protocols::symmetric_docking::SymDockProtocol::operator=(const class protocols::symmetric_docking::SymDockProtocol &) –> class protocols::symmetric_docking::SymDockProtocol &

calc_CAPRI_rank(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, Irmsd: float, Lrmsd: float, Fnat: float) float

Calculate fraction of native contacts recovered for one chain assuming correct native chain order

C++: protocols::symmetric_docking::SymDockProtocol::calc_CAPRI_rank(const double, const double, const double) –> double

calc_Irms(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate interface RMSD of one chain to symmetric starting structure assuming correct native chain order

C++: protocols::symmetric_docking::SymDockProtocol::calc_Irms(class core::pose::Pose &) –> double

calc_fnat(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, dock_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) float

Calculate fraction of native contacts recovered for one chain assuming correct native chain order

C++: protocols::symmetric_docking::SymDockProtocol::calc_fnat(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>) –> double

calc_interaction_energy(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate Interaction energy between partners

C++: protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(class core::pose::Pose &) –> double

calc_res_contact(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, dist_cutoff: float) bool

Calculate whether two residues are within a distance cutoff of each other

C++: protocols::symmetric_docking::SymDockProtocol::calc_res_contact(const class std::shared_ptr<class core::conformation::Residue>, const class std::shared_ptr<class core::conformation::Residue>, const double) –> bool

calc_rms(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float

Calculate RMSD from partner to symmetric starting structure

C++: protocols::symmetric_docking::SymDockProtocol::calc_rms(class core::pose::Pose &) –> double

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.symmetric_docking.SymDockProtocol) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::symmetric_docking::SymDockProtocol::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>

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, des: bool) -> None

Turn on Design of partner 2 during docking - not thoroughly tested

I think this is just copied over from regular docking protocol?

C++: protocols::symmetric_docking::SymDockProtocol::design(const bool) –> void

  1. design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) -> bool

C++: protocols::symmetric_docking::SymDockProtocol::design() const –> bool

docking_highres_filter(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::symmetric_docking::SymDockProtocol::docking_highres_filter(class core::pose::Pose &) –> bool

docking_lowres_filter(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(class core::pose::Pose &) –> bool

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.symmetric_docking.SymDockProtocol) str

C++: protocols::symmetric_docking::SymDockProtocol::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

hurry(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, hurry: bool) None

Skip population of the score map

C++: protocols::symmetric_docking::SymDockProtocol::hurry(const bool) –> void

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::symmetric_docking::SymDockProtocol::mover_name() –> std::string

static name() str

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

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

RosettaScripts Methods //////

C++: protocols::symmetric_docking::SymDockProtocol::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::symmetric_docking::SymDockProtocol::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recover_sidechains(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose) None

Recover sidechains from the native pose

C++: protocols::symmetric_docking::SymDockProtocol::recover_sidechains(class core::pose::Pose &, const class core::pose::Pose &) –> void

register_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) None

Register Options from the Commandline

C++: protocols::symmetric_docking::SymDockProtocol::register_options() –> void

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

each use.

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

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

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

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

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

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

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

score_only(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None

Only score the pose using docking config

C++: protocols::symmetric_docking::SymDockProtocol::score_only(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol) None

Setup options based on constructors

C++: protocols::symmetric_docking::SymDockProtocol::set_default() –> void

set_dock_ppk(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, dock_ppk_in: bool) None

C++: protocols::symmetric_docking::SymDockProtocol::set_dock_ppk(bool) –> void

set_dock_rtmin(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, dock_rtmin_in: bool) None

Setters for Protocol Options

C++: protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin(bool) –> void

set_fullatom(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, fullatom_in: bool) None

C++: protocols::symmetric_docking::SymDockProtocol::set_fullatom(const bool) –> void

set_highres_scorefxn(*args, **kwargs)

Overloaded function.

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_high_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

  1. set_highres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_high_in: pyrosetta.rosetta.core.scoring.ScoreFunction, docking_score_pack_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_local_refine(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, local_refine_in: bool) None

C++: protocols::symmetric_docking::SymDockProtocol::set_local_refine(const bool) –> void

set_lowres_scorefxn(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, docking_score_low_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_max_repeats(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, max_repeats_in: int) None

C++: protocols::symmetric_docking::SymDockProtocol::set_max_repeats(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_sc_min(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, sc_min_in: bool) None

C++: protocols::symmetric_docking::SymDockProtocol::set_sc_min(bool) –> 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

set_view(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, view_in: bool) None

C++: protocols::symmetric_docking::SymDockProtocol::set_view(bool) –> void

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocol, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

Set Task Factory for Packing

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

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

C++: protocols::symmetric_docking::SymDockProtocol::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &

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.symmetric_docking.SymDockProtocolCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator

C++: protocols::symmetric_docking::SymDockProtocolCreator::operator=(const class protocols::symmetric_docking::SymDockProtocolCreator &) –> class protocols::symmetric_docking::SymDockProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator) str

C++: protocols::symmetric_docking::SymDockProtocolCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockProtocolCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

pyrosetta.rosetta.protocols.symmetric_docking.SymDock_main() None

Define Main funciton for symmetric docking protocol

C++: protocols::symmetric_docking::SymDock_main() –> void

class pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingHiRes::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes

C++: protocols::symmetric_docking::SymDockingHiRes::operator=(const class protocols::symmetric_docking::SymDockingHiRes &) –> class protocols::symmetric_docking::SymDockingHiRes &

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.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::symmetric_docking::SymDockingHiRes::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>

design(*args, **kwargs)

Overloaded function.

  1. design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, des: bool) -> None

C++: protocols::symmetric_docking::SymDockingHiRes::design(const bool) –> void

  1. design(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) -> bool

C++: protocols::symmetric_docking::SymDockingHiRes::design() const –> bool

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_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::symmetric_docking::SymDockingHiRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) str

C++: protocols::symmetric_docking::SymDockingHiRes::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

set_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_default(class core::pose::Pose &) –> void

set_dock_mcm_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol(class core::pose::Pose &) –> void

set_dock_min_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_min_protocol() –> void

set_dock_ppk_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol(class core::pose::Pose &) –> 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_type(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, min_type_in: str) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_min_type(std::string) –> void

set_move_map(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_move_map(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

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

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

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

set_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_protocol(class core::pose::Pose &) –> void

set_repack(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, repack_switch: bool) None

C++: protocols::symmetric_docking::SymDockingHiRes::set_repack(bool) –> void

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

task_factory(*args, **kwargs)

Overloaded function.

  1. task_factory(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingHiRes, task: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

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

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

C++: protocols::symmetric_docking::SymDockingHiRes::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &

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.symmetric_docking.SymDockingLowRes

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, : pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes

C++: protocols::symmetric_docking::SymDockingLowRes::operator=(const class protocols::symmetric_docking::SymDockingLowRes &) –> class protocols::symmetric_docking::SymDockingLowRes &

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.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.Mover

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::symmetric_docking::SymDockingLowRes::get_mc() –> class std::shared_ptr<class protocols::moves::MonteCarlo>

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) str

C++: protocols::symmetric_docking::SymDockingLowRes::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_pymol_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes) pyrosetta.rosetta.protocols.moves.PyMOLMover

C++: protocols::symmetric_docking::SymDockingLowRes::get_pymol_mover() –> class std::shared_ptr<class protocols::moves::PyMOLMover>

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

rigid_body_trial(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::rigid_body_trial(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::set_default(class core::pose::Pose &) –> void

set_default_mc(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::set_default_mc(class core::pose::Pose &) –> void

set_default_move_map(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::set_default_move_map(class core::pose::Pose &) –> void

set_default_protocol(self: pyrosetta.rosetta.protocols.symmetric_docking.SymDockingLowRes, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymDockingLowRes::set_default_protocol(class core::pose::Pose &) –> 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.symmetric_docking.SymFoldandDockMoveRbJumpMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::operator=(const class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover &) –> class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMover) str

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::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::symmetric_docking::SymFoldandDockMoveRbJumpMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMover::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::symmetric_docking::SymFoldandDockMoveRbJumpMover::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.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator) str

C++: protocols::symmetric_docking::SymFoldandDockMoveRbJumpMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockMoveRbJumpMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::operator=(const class protocols::symmetric_docking::SymFoldandDockRbTrialMover &) –> class protocols::symmetric_docking::SymFoldandDockRbTrialMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover) str

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMover) None

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::init() –> void

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

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

static mover_name() str

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMover::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::symmetric_docking::SymFoldandDockRbTrialMover::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.symmetric_docking.SymFoldandDockRbTrialMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator) str

C++: protocols::symmetric_docking::SymFoldandDockRbTrialMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockRbTrialMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::operator=(const class protocols::symmetric_docking::SymFoldandDockSlideTrialMover &) –> class protocols::symmetric_docking::SymFoldandDockSlideTrialMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMover) str

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::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::symmetric_docking::SymFoldandDockSlideTrialMover::mover_name() –> std::string

static name() str

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

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

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMover::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::symmetric_docking::SymFoldandDockSlideTrialMover::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.symmetric_docking.SymFoldandDockSlideTrialMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator, : pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::operator=(const class protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator &) –> class protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator) str

C++: protocols::symmetric_docking::SymFoldandDockSlideTrialMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.symmetric_docking.SymFoldandDockSlideTrialMoverCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover

Bases: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover) pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover

C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::operator=(const class protocols::symmetric_docking::SymInterfaceSidechainMinMover &) –> class protocols::symmetric_docking::SymInterfaceSidechainMinMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover) str

C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

set_default_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover) None

C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::set_default_options() –> 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_interface_dist(self: pyrosetta.rosetta.protocols.symmetric_docking.SymInterfaceSidechainMinMover, interface_dist_in: float) None

C++: protocols::symmetric_docking::SymInterfaceSidechainMinMover::set_interface_dist(double) –> void

set_minmover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, minmover_in: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None

C++: protocols::symmetric_docking::SymSidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> 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 &

update_movemap(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymSidechainMinMover::update_movemap(class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::symmetric_docking::SymRestrictTaskForDocking::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking, : pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking) pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking

C++: protocols::symmetric_docking::SymRestrictTaskForDocking::operator=(const class protocols::symmetric_docking::SymRestrictTaskForDocking &) –> class protocols::symmetric_docking::SymRestrictTaskForDocking &

clone(self: pyrosetta.rosetta.protocols.symmetric_docking.SymRestrictTaskForDocking) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::symmetric_docking::SymRestrictTaskForDocking::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

class pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymSidechainMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, : pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover) pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover

C++: protocols::symmetric_docking::SymSidechainMinMover::operator=(const class protocols::symmetric_docking::SymSidechainMinMover &) –> class protocols::symmetric_docking::SymSidechainMinMover &

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

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

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

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

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

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

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

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover) str

C++: protocols::symmetric_docking::SymSidechainMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

set_default_options(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover) None

C++: protocols::symmetric_docking::SymSidechainMinMover::set_default_options() –> 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_minmover(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, minmover_in: pyrosetta.rosetta.protocols.minimization_packing.MinMover) None

C++: protocols::symmetric_docking::SymSidechainMinMover::set_minmover(class std::shared_ptr<class protocols::minimization_packing::MinMover>) –> 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 &

update_movemap(self: pyrosetta.rosetta.protocols.symmetric_docking.SymSidechainMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::symmetric_docking::SymSidechainMinMover::update_movemap(class core::pose::Pose &) –> void