loop_modeling

• refiners
• samplers
• utilities

Bindings for protocols::loop_modeling namespace

class pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest

Bases: pybind11_object

Represent the types of fold tree supported by LoopMover.

This enum supports the bitwise and and or operators. Strictly speaking, this is an abuse of enum because both operators can return values that are not contained in the enum. But this design meets two key requirements. First, programmers have to work with the enumerated values. Second, bitwise logic can be used to easily combine flags and to determine how composite requests should be satisfied.

Members:

FTR_LOOPS_WITH_CUTS

FTR_SIMPLE_TREE

FTR_DONT_CARE

FTR_DONT_CARE = <FoldTreeRequest.FTR_DONT_CARE: 255>

FTR_LOOPS_WITH_CUTS = <FoldTreeRequest.FTR_LOOPS_WITH_CUTS: 1>

FTR_SIMPLE_TREE = <FoldTreeRequest.FTR_SIMPLE_TREE: 2>

property name

property value

class pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder

Bases: LoopMover

Build loops from scratch.

Kale Kundert

Roland A. Pache, PhD

Building a loop from scratch is useful in two scenarios. The first is when there’s missing density that needs to be modeled, and the second is when the whole loop modeling algorithm needs to be benchmarked. This mover uses kinematic closure (KIC) to build loops. By default, the loop are built by picking phi and psi values from a Ramachandran distribution and setting all other DOFs to ideal values. Phi and psi values can also be picked using fragment libraries. Loop building succeeds when a model is found that passes a more-lenient-than-usual bump check. If no such model is found after 1000 iterations, the mover gives up and reports failure.

This process can be very slow for long loops, because there’s nothing guiding the algorithm towards the right solution. By default, torsions are just being randomly picked, and they often won’t fit in the relatively narrow space that’s available. The problem is worse for interior loops than it is for surface loops, of course. This algorithm seems to work well enough on 12 residue loops, but beyond that it may be necessary to develop a smarter algorithm that preferentially builds into free space.

apply(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sample the pose in the regions specified by get_loops().

The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.

C++: protocols::loop_modeling::LoopMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder, : pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder) → pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder

C++: protocols::loop_modeling::LoopBuilder::operator=(const class protocols::loop_modeling::LoopBuilder &) –> class protocols::loop_modeling::LoopBuilder &

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>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition, ct_gen: utility::tag::XMLSchemaComplexTypeGenerator, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None

C++: protocols::loop_modeling::LoopMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaComplexTypeGenerator &, class utility::tag::XMLSchemaSimpleSubelementList &) –> void

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

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

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

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

fpd

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

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

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

get_children_names(*args, **kwargs)

Overloaded function.

1. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

Add the names of all the algorithms invoked by this loop mover to

the given list. Indentation is used to represent hierarchy.

C++: protocols::loop_modeling::LoopMover::get_children_names(class utility::vector1<std::string, class std::allocator<std::string > > &, std::string) const –> void

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_logger(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder) → protocols::loop_modeling::utilities::TrajectoryLogger

Return the object that report on the progress of the protocol.

C++: protocols::loop_modeling::LoopBuilder::get_logger() const –> class std::shared_ptr<class protocols::loop_modeling::utilities::TrajectoryLogger>

get_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, index: int) → pyrosetta.rosetta.protocols.loops.Loop

Return the specified loop.

C++: protocols::loop_modeling::LoopMover::get_loop(unsigned long) const –> const class protocols::loops::Loop &

get_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loops.Loops

Return the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::get_loops() –> class std::shared_ptr<class protocols::loops::Loops>

get_max_attempts(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder) → int

Return the number of times KIC will be invoked before the

LoopBuilder gives up.

C++: protocols::loop_modeling::LoopBuilder::get_max_attempts() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder) → str

C++: protocols::loop_modeling::LoopBuilder::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_score_function(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder) → pyrosetta.rosetta.core.scoring.ScoreFunction

Get the score function to be used on the next call to apply().

C++: protocols::loop_modeling::LoopBuilder::get_score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

static get_score_function_attributes(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None

C++: protocols::loop_modeling::LoopBuilder::get_score_function_attributes(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

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::loop_modeling::LoopBuilder::mover_name() –> std::string

static name() → str

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

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

Configure from a RosettaScripts tag.

C++: protocols::loop_modeling::LoopBuilder::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::loop_modeling::LoopBuilder::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

request_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest

Return an enum representing the kind of fold tree that is

compatible with this mover.

The FoldTreeRequest enum values can be combined using the bitwise logical operators. For example, you can request either the standard fold tree or a simple fold tree with FTR_LOOPS_WITH_CUTS | FTR_SIMPLE_TREE.

C++: protocols::loop_modeling::LoopMover::request_fold_tree() const –> enum protocols::loop_modeling::FoldTreeRequest

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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Set the loop to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(*args, **kwargs)

Overloaded function.

1. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(const class protocols::loops::Loops &) –> void

set_max_attempts(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder, attempts: int) → None

Specify how many time to invoke KIC before giving up.

C++: protocols::loop_modeling::LoopBuilder::set_max_attempts(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_score_function(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the score function to be used on the next call to apply().

C++: protocols::loop_modeling::LoopBuilder::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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

static setup_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, request: pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest) → None

Setup the given pose with a fold tree that is compatible with the

given loops and requests.

C++: protocols::loop_modeling::LoopMover::setup_fold_tree(class core::pose::Pose &, class std::shared_ptr<const class protocols::loops::Loops>, enum protocols::loop_modeling::FoldTreeRequest) –> 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

trust_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Promise that the calling code will setup a fold tree compatible

with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called.

C++: protocols::loop_modeling::LoopMover::trust_fold_tree() –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_fragments(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilder, frag_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_fragment_FragSet_t) → None

Use the given fragment libraries when building the loop.

C++: protocols::loop_modeling::LoopBuilder::use_fragments(const class utility::vector1<class std::shared_ptr<const class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<const class core::fragment::FragSet> > > &) –> void

was_successful(*args, **kwargs)

Overloaded function.

1. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) -> bool

Return true if the previous move was successful.

C++: protocols::loop_modeling::LoopMover::was_successful() const –> bool

2. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, value: bool) -> None

Set the success status of a loop mover

C++: protocols::loop_modeling::LoopMover::was_successful(bool) –> void

class pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator, : pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator) → pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator

C++: protocols::loop_modeling::LoopBuilderCreator::operator=(const class protocols::loop_modeling::LoopBuilderCreator &) –> class protocols::loop_modeling::LoopBuilderCreator &

create_mover(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.loop_modeling.LoopBuilderCreator) → str

C++: protocols::loop_modeling::LoopBuilderCreator::keyname() const –> std::string

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

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

class pyrosetta.rosetta.protocols.loop_modeling.LoopMover

Bases: Mover

Base class for loop-sampling algorithms.

Classes that inherit from LoopMover can plug into the LoopProtocol framework. The only method that subclasses need to provide is do_apply(). Note that the apply() method itself cannot be overwritten, because LoopMover uses it to do some useful setup and teardown work. Instead, there are two versions of do_apply() that subclasses may implement. Both return a boolean to indicate whether or not the move succeeded. The first version of do_apply() accepts only a Pose and is expected to operate on all of the loops returned by get_loops(). The second version accepts a Pose and a Loop, and is only expected to operate on the given loop. By default, the first version simply iterates through the loops provided by get_loops() and calls the second version on each one. This means that if the first version is overwritten, the second version will no longer be called. If neither method is reimplemented, a runtime error will be thrown.

LoopMover provides a handful of features that could be useful to a loop sampling algorithm. As mentioned above, the get_loops() method returns the loops that should be sampled. There are also a number of methods provided for controlling how the fold tree is setup up. The request_fold_tree() method can be reimplemented to return an enum telling what kind of fold tree this mover requires. When apply() is called for the first time, a compatible fold tree will be configured. This behavior is disabled if trust_fold_tree() is called beforehand, in which case responsibility for constructing a compatible fold tree is passed to the calling code.

apply(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sample the pose in the regions specified by get_loops().

The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.

C++: protocols::loop_modeling::LoopMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, : pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loop_modeling.LoopMover

C++: protocols::loop_modeling::LoopMover::operator=(const class protocols::loop_modeling::LoopMover &) –> class protocols::loop_modeling::LoopMover &

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>

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition, ct_gen: utility::tag::XMLSchemaComplexTypeGenerator, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None

C++: protocols::loop_modeling::LoopMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaComplexTypeGenerator &, class utility::tag::XMLSchemaSimpleSubelementList &) –> void

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

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

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

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

fpd

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

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

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

get_children_names(*args, **kwargs)

Overloaded function.

1. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

Add the names of all the algorithms invoked by this loop mover to

the given list. Indentation is used to represent hierarchy.

C++: protocols::loop_modeling::LoopMover::get_children_names(class utility::vector1<std::string, class std::allocator<std::string > > &, std::string) const –> void

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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, index: int) → pyrosetta.rosetta.protocols.loops.Loop

Return the specified loop.

C++: protocols::loop_modeling::LoopMover::get_loop(unsigned long) const –> const class protocols::loops::Loop &

get_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loops.Loops

Return the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::get_loops() –> class std::shared_ptr<class protocols::loops::Loops>

get_name(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → str

Return the name of this mover.

C++: protocols::loop_modeling::LoopMover::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_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.loop_modeling.LoopMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Configure from a RosettaScripts tag.

C++: protocols::loop_modeling::LoopMover::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

request_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest

Return an enum representing the kind of fold tree that is

compatible with this mover.

The FoldTreeRequest enum values can be combined using the bitwise logical operators. For example, you can request either the standard fold tree or a simple fold tree with FTR_LOOPS_WITH_CUTS | FTR_SIMPLE_TREE.

C++: protocols::loop_modeling::LoopMover::request_fold_tree() const –> enum protocols::loop_modeling::FoldTreeRequest

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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Set the loop to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(*args, **kwargs)

Overloaded function.

1. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(const class protocols::loops::Loops &) –> 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

static setup_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, request: pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest) → None

Setup the given pose with a fold tree that is compatible with the

given loops and requests.

C++: protocols::loop_modeling::LoopMover::setup_fold_tree(class core::pose::Pose &, class std::shared_ptr<const class protocols::loops::Loops>, enum protocols::loop_modeling::FoldTreeRequest) –> 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

trust_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Promise that the calling code will setup a fold tree compatible

with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called.

C++: protocols::loop_modeling::LoopMover::trust_fold_tree() –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

was_successful(*args, **kwargs)

Overloaded function.

1. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) -> bool

Return true if the previous move was successful.

C++: protocols::loop_modeling::LoopMover::was_successful() const –> bool

2. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, value: bool) -> None

Set the success status of a loop mover

C++: protocols::loop_modeling::LoopMover::was_successful(bool) –> void

class pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol

Bases: LoopMover

Monte Carlo search for low energy loop conformations.

This class provides an easy way to run a Monte Carlo simulation searching for the lowest energy conformations for a set of loops. This simulation is organized into three nested loops. On each iteration of the outermost loop, the lowest scoring pose is recovered and the repulsive terms in the score function may be ramped (although this ramping is disabled by default). On each iteration of the intermediate loop, the temperature may be ramped (this ramping is enabled by default). And on each iteration of the innermost loop, a new conformation is sampled and either accepted or rejected according to the Metropolis criterion. The intermediate loop usually goes through more than 100 iterations, while the innermost and outermost loops only go through less than 5.

Like any mover, all the work is done by the apply() method. The rest of the methods of this class are just getters and setters that can be used to control various aspects of the simulation. The add_mover(), add_filter(), and add_acceptance_check() methods are worth drawing some attention to. These methods are used to build up the group of LoopMover objects that samples new loop conformations in the innermost loop. The movers are guaranteed to be applied in the order they are added to the protocol.

add_acceptance_check(*args, **kwargs)

Overloaded function.

1. add_acceptance_check(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) -> None

2. add_acceptance_check(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, name: str) -> None

Add an acceptance check to the simulation.

An acceptance check is always performed after all the loop movers have been applied, unless one of the movers failed. This method allows additional acceptance checks to be included in the protocol by adding a loop mover that does nothing but make that check.

C++: protocols::loop_modeling::LoopProtocol::add_acceptance_check(std::string) –> void

add_filter(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, filter: pyrosetta.rosetta.protocols.filters.Filter) → None

Add a Filter to the simulation.

C++: protocols::loop_modeling::LoopProtocol::add_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

add_mover(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, mover: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Add a LoopMover to the simulation.

Loop movers will be applied in the order they’re added.

add_refiner()

mark_as_default()

C++: protocols::loop_modeling::LoopProtocol::add_mover(class std::shared_ptr<class protocols::loop_modeling::LoopMover>) –> void

add_refiner(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, refiner: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Add a LoopMover to the simulation as a refiner.

This method is very similar to add_mover(). Both methods add a new LoopMover to the simulation. This difference is subtle, but relevant when a LoopProtocol is being filled with a default set of movers that might be modified later.

This situation arises when a LoopModeler object is being constructed, or when a <LoopModeler> tag is being parsed by rosetta scripts. In both of these cases, centroid and fullatom LoopProtocols are created right away and filled with default movers. This avoids the necessity of specifying all the usual movers every time loop modeling is invoked. But the default movers may be subsequently overridden. In this case, there is a difference between LoopMovers added via add_mover() (i.e. movers) and add_refiner() (i.e. refiners).

The difference is that movers can be marked as “default” and then be implicitly overridden. Consider the following sequence of calls:

protocol->add_mover(new CcdMover); protocol->mark_as_default(); protocol->add_mover(new KicMover);

This will result in a LoopProtocol containing only a KicMover. When mark_as_default() is called, all movers within the protocol are set to be replaced the next time add_mover() is called. You can think of those movers as being part of a default configuration that should be replaced when a new configuration is given.

Refiners are not affected by mark_as_default(). Calling add_refiner() will always add a refiner and will never remove old ones, although old refiners can be explicitly removed with clear_refiners(). Refiners are also applied after movers, regardless of the order in which add_mover() and add_refiner() were called. The purpose of all this is to make it easy to replace the parts of a LoopProtocol that are more variable without having to also replace those that are more static.

The variable part of a LoopProtocol is typically the sampling algorithm: KIC or CCD, often with myriad options. The static part is typically the refinement algorithm: minimization, rotamer trials, and repacking, all with carefully tuned parameters. Using add_mover(), mark_as_default(), and add_refiner() makes it easy to change the sampling algorithm without having to worry about the refinement algorithm.

add_mover()

mark_as_default()

C++: protocols::loop_modeling::LoopProtocol::add_refiner(class std::shared_ptr<class protocols::loop_modeling::LoopMover>) –> void

apply(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Sample the pose in the regions specified by get_loops().

The parent class apply() method automatically sets up a fold tree (if necessary) and keeps track of whether or not the move succeeded. Child classes should reimplement do_apply() instead of this method.

C++: protocols::loop_modeling::LoopMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, : pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol

C++: protocols::loop_modeling::LoopProtocol::operator=(const class protocols::loop_modeling::LoopProtocol &) –> class protocols::loop_modeling::LoopProtocol &

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

clear_movers(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → None

Remove all movers from the protocol.

add_mover()

add_refiner()

clear_refiners()

clear_movers_and_refiners()

C++: protocols::loop_modeling::LoopProtocol::clear_movers() –> void

clear_movers_and_refiners(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → None

Remove all movers and refiners from the protocol.

add_mover()

add_refiner()

clear_movers()

clear_refiners()

C++: protocols::loop_modeling::LoopProtocol::clear_movers_and_refiners() –> void

clear_refiners(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → None

Remove all refiners from the protocol.

add_mover()

add_refiner()

clear_movers()

clear_movers_and_refiners()

C++: protocols::loop_modeling::LoopProtocol::clear_refiners() –> 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>

static complex_type_generator_for_loop_protocol(xsd: utility::tag::XMLSchemaDefinition) → utility::tag::XMLSchemaComplexTypeGenerator

C++: protocols::loop_modeling::LoopProtocol::complex_type_generator_for_loop_protocol(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

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

static define_composition_schema(xsd: utility::tag::XMLSchemaDefinition, ct_gen: utility::tag::XMLSchemaComplexTypeGenerator, subelements: utility::tag::XMLSchemaSimpleSubelementList) → None

C++: protocols::loop_modeling::LoopMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &, class utility::tag::XMLSchemaComplexTypeGenerator &, class utility::tag::XMLSchemaSimpleSubelementList &) –> void

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

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

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

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

fpd

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

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

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

get_children_names(*args, **kwargs)

Overloaded function.

1. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string) -> None

2. get_children_names(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, names: pyrosetta.rosetta.utility.vector1_std_string, indent: str) -> None

Add the names of all the algorithms invoked by this loop mover to

the given list. Indentation is used to represent hierarchy.

C++: protocols::loop_modeling::LoopMover::get_children_names(class utility::vector1<std::string, class std::allocator<std::string > > &, std::string) const –> void

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_logger(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → protocols::loop_modeling::utilities::TrajectoryLogger

Return the object that report on the progress of the protocol.

C++: protocols::loop_modeling::LoopProtocol::get_logger() const –> class std::shared_ptr<class protocols::loop_modeling::utilities::TrajectoryLogger>

get_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, index: int) → pyrosetta.rosetta.protocols.loops.Loop

Return the specified loop.

C++: protocols::loop_modeling::LoopMover::get_loop(unsigned long) const –> const class protocols::loops::Loop &

get_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loops.Loops

Return the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::get_loops() –> class std::shared_ptr<class protocols::loops::Loops>

get_mover_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → int

Return how many times the loops movers will be invoked after the

score function and temperature have been updated.

C++: protocols::loop_modeling::LoopProtocol::get_mover_cycles() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → str

C++: protocols::loop_modeling::LoopProtocol::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_score_function(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

Get the score function to be used on the next call to apply().

C++: protocols::loop_modeling::LoopProtocol::get_score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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_sfxn_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → int

Get the number of iterations the loop that ramps the score

function will make.

C++: protocols::loop_modeling::LoopProtocol::get_sfxn_cycles() const –> unsigned long

get_temp_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → int

Get the number of iterations the loop that ramps the temperature

should make.

This will throw an exception if the ‘times_loop_length’ argument was passed to set_temp_cycles() and no loop has been specified yet. The value returned will always be the actual number of iterations that will be carried out.

C++: protocols::loop_modeling::LoopProtocol::get_temp_cycles() const –> unsigned long

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 loop_protocol_attlist() → pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t

C++: protocols::loop_modeling::LoopProtocol::loop_protocol_attlist() –> class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> >

mark_as_default(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → None

Indicate that every mover that is currently part of the protocol

should be removed the next time a mover is added.

add_mover()

add_refiner()

C++: protocols::loop_modeling::LoopProtocol::mark_as_default() –> void

mark_as_test_run(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol) → None

Indicate that this protocol is being used for a test run.

This method simply limits the number of iterations that will be performed. It can be “undone” by explicitly setting the score function, temperature, and mover cycles back to normal values.

C++: protocols::loop_modeling::LoopProtocol::mark_as_test_run() –> void

static mover_name() → str

C++: protocols::loop_modeling::LoopProtocol::mover_name() –> std::string

static name() → str

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

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

LoopMover::parse_my_tag

C++: protocols::loop_modeling::LoopProtocol::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::loop_modeling::LoopProtocol::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

request_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest

Return an enum representing the kind of fold tree that is

compatible with this mover.

The FoldTreeRequest enum values can be combined using the bitwise logical operators. For example, you can request either the standard fold tree or a simple fold tree with FTR_LOOPS_WITH_CUTS | FTR_SIMPLE_TREE.

C++: protocols::loop_modeling::LoopMover::request_fold_tree() const –> enum protocols::loop_modeling::FoldTreeRequest

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_cst_term_ramping(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, value: bool) → None

Enable or disable ramping of constraints terms of the score

funciton.

C++: protocols::loop_modeling::LoopProtocol::set_cst_term_ramping(bool) –> 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_loop(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

Set the loop to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loop(const class protocols::loops::Loop &) –> void

set_loops(*args, **kwargs)

Overloaded function.

1. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(class std::shared_ptr<class protocols::loops::Loops>) –> void

2. set_loops(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, loops: pyrosetta.rosetta.protocols.loops.Loops) -> None

Set the loops to be sampled on the next call to apply().

C++: protocols::loop_modeling::LoopMover::set_loops(const class protocols::loops::Loops &) –> void

set_mover_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, x: int) → None

Specify how many times the loops movers should be invoked after

the score function and temperature have been updated.

The mover loop is the innermost loop. It is contained by the score function loop and the temperature loop.

C++: protocols::loop_modeling::LoopProtocol::set_mover_cycles(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_rama_term_ramping(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, value: bool) → None

Enable or disable ramping the repulsive term of the score

function.

C++: protocols::loop_modeling::LoopProtocol::set_rama_term_ramping(bool) –> void

set_repulsive_term_ramping(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, value: bool) → None

Enable or disable ramping the repulsive term of the score

function.

C++: protocols::loop_modeling::LoopProtocol::set_repulsive_term_ramping(bool) –> void

set_score_function(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the score function to be used on the next call to apply().

C++: protocols::loop_modeling::LoopProtocol::set_score_function(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_sfxn_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, x: int) → None

Set the number of iterations the loop that ramps the score

function should make.

The score function loop is the outermost loop. It contains the temperature loop and the mover loop.

C++: protocols::loop_modeling::LoopProtocol::set_sfxn_cycles(unsigned long) –> void

set_temp_cycles(*args, **kwargs)

Overloaded function.

1. set_temp_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, x: int) -> None

2. set_temp_cycles(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, x: int, times_loop_length: bool) -> None

Set the number of iterations the loop that ramps the temperature

should make.

The temperature loop is contained by the score function loop. It contains the mover loop. If the second boolean argument is true, the number of iterations will be the first value times the combined length of all the loops being sampled.

C++: protocols::loop_modeling::LoopProtocol::set_temp_cycles(unsigned long, bool) –> void

set_temperature_ramping(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, value: bool) → None

Enable or disable temperature ramping in this simulation.

C++: protocols::loop_modeling::LoopProtocol::set_temperature_ramping(bool) –> void

set_temperature_schedule(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocol, start: float, stop: float) → None

Set the initial and final temperatures for the simulation.

The temperature will be linearly interpolated between these values during the simulation.

C++: protocols::loop_modeling::LoopProtocol::set_temperature_schedule(double, double) –> 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

static setup_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops, request: pyrosetta.rosetta.protocols.loop_modeling.FoldTreeRequest) → None

Setup the given pose with a fold tree that is compatible with the

given loops and requests.

C++: protocols::loop_modeling::LoopMover::setup_fold_tree(class core::pose::Pose &, class std::shared_ptr<const class protocols::loops::Loops>, enum protocols::loop_modeling::FoldTreeRequest) –> 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

trust_fold_tree(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) → None

Promise that the calling code will setup a fold tree compatible

with request_fold_tree(). If this method is not called, this mover will setup a fold tree on its own every time apply() is called.

C++: protocols::loop_modeling::LoopMover::trust_fold_tree() –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

was_successful(*args, **kwargs)

Overloaded function.

1. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover) -> bool

Return true if the previous move was successful.

C++: protocols::loop_modeling::LoopMover::was_successful() const –> bool

2. was_successful(self: pyrosetta.rosetta.protocols.loop_modeling.LoopMover, value: bool) -> None

Set the success status of a loop mover

C++: protocols::loop_modeling::LoopMover::was_successful(bool) –> void

class pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator, : pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator) → pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator

C++: protocols::loop_modeling::LoopProtocolCreator::operator=(const class protocols::loop_modeling::LoopProtocolCreator &) –> class protocols::loop_modeling::LoopProtocolCreator &

create_mover(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.loop_modeling.LoopProtocolCreator) → str

C++: protocols::loop_modeling::LoopProtocolCreator::keyname() const –> std::string

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

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

class pyrosetta.rosetta.protocols.loop_modeling.ToolboxKeys

Bases: pybind11_object

Key names for data shared between loop movers.