movers

Bindings for protocols::trRosetta_protocols::movers namespace

class pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode

Bases: pybind11_builtins.pybind11_object

The modes for minimizing the backbone.

If a developer adds an entry to this list, she or he should be sure to update trRosettaProtocolMover::get_minimization_mode_string_from_enum(). Also, the basic/options/options_rosetta.py “trRosetta” OptionGroup should have the new options added to the “backbone_minimization_mode” option.

Members:

classic0

classic1

classic2

NUM_ENTRIES

NUM_ENTRIES = <trRosettaProtocolBackboneMinimizationMode.classic2: 3>
classic0 = <trRosettaProtocolBackboneMinimizationMode.classic0: 1>
classic1 = <trRosettaProtocolBackboneMinimizationMode.classic1: 2>
classic2 = <trRosettaProtocolBackboneMinimizationMode.classic2: 3>
property name
class pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode

Bases: pybind11_builtins.pybind11_object

The modes for randomizing backbone dihedrals.

If a developer adds an entry to this list, she or he should be sure to update trRosettaProtocolMover::get_randomization_mode_string_from_enum(). Also, the basic/options/options_rosetta.py “trRosetta” OptionGroup should have the new options added to the “backbone_randomization_mode” option.

Members:

classic

ramachandran

bins

NUM_ENTRIES

NUM_ENTRIES = <trRosettaProtocolBackboneRandomizationMode.bins: 3>
bins = <trRosettaProtocolBackboneRandomizationMode.bins: 3>
classic = <trRosettaProtocolBackboneRandomizationMode.classic: 1>
property name
ramachandran = <trRosettaProtocolBackboneRandomizationMode.ramachandran: 2>
class pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

The full trRosetta structure prediction protocol from Yang et al, converted to C++ and implemented as a mover.

Vikram K. Mulligan (vmulligan.org)

apply(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover, pose: pyrosetta.rosetta.core.pose.Pose) None

Apply the mover

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover, : pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover) pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::operator=(const class protocols::trRosetta_protocols::movers::trRosettaProtocolMover &) –> class protocols::trRosetta_protocols::movers::trRosettaProtocolMover &

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.trRosetta_protocols.movers.trRosettaProtocolMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::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.trRosetta_protocols.movers.trRosettaProtocolMover) pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::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

static get_minimization_mode_enum_from_string(mode_name: str) pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode

Given a backbone minimization mode name, get the enum corresponding to the name.

Throws if an invalid name is provided.

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_minimization_mode_enum_from_string(const std::string &) –> enum protocols::trRosetta_protocols::movers::trRosettaProtocolBackboneMinimizationMode

static get_minimization_mode_string_from_enum(mode_enum: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneMinimizationMode) str

Given a backbone minimization mode enum, get a string corresponding to the enum.

This function must be updated if entries are added to the trRosettaProtocolBackboneMinimizationMode enum class!

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_minimization_mode_string_from_enum(const enum protocols::trRosetta_protocols::movers::trRosettaProtocolBackboneMinimizationMode) –> std::string

get_name(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover) str

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::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>

static get_randomization_mode_enum_from_string(mode_name: str) pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode

Given a backbone randomization mode name, get the enum corresponding to the name.

Throws if an invalid name is provided.

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_randomization_mode_enum_from_string(const std::string &) –> enum protocols::trRosetta_protocols::movers::trRosettaProtocolBackboneRandomizationMode

static get_randomization_mode_string_from_enum(mode_enum: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolBackboneRandomizationMode) str

Given a backbone randomization mode enum, get a string corresponding to the enum.

This function must be updated if entries are added to the trRosettaProtocolBackboneRandomizationMode enum class!

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::get_randomization_mode_string_from_enum(const enum protocols::trRosetta_protocols::movers::trRosettaProtocolBackboneRandomizationMode) –> std::string

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_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::trRosetta_protocols::movers::trRosettaProtocolMover::mover_name() –> std::string

static name() str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

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

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

provide_citation_info(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
This mover is unpublished. It returns Vikram K. Mulligan as its author.

It also adds Yang et al. (2020) as a citiation for trRosetta itself.

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options(*args, **kwargs)

Overloaded function.

  1. register_options() -> None

  2. register_options(only_constraint_generator_options: bool) -> None

Indicate commandline flags that are relevant to this mover.

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::register_options(const bool) –> 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.trRosetta_protocols.movers.trRosettaProtocolMover) -> None

  2. show(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMover::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.trRosetta_protocols.movers.trRosettaProtocolMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator, : pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator) pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator::operator=(const class protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator &) –> class protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator) str

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.trRosetta_protocols.movers.trRosettaProtocolMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) None

C++: protocols::trRosetta_protocols::movers::trRosettaProtocolMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void