abinitio

• abscript

Bindings for protocols::abinitio namespace

class pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication

Bases: pybind11_builtins.pybind11_object

application level code for Abrelax, Foldconstraints and JumpingFoldconstraints WARNING WARNING WARNING. THREAD UNSAFE. INVOKES ConstraintFactory::replace_creator. CODE THAT ABUSES SINGLETONS LIKE THIS OUGHT TO BE SHOT.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, arg0: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_constraints(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, pose: pyrosetta.rosetta.core.pose.Pose) → None

read constraint set (self-initializing) and connect it to pose

C++: protocols::abinitio::AbrelaxApplication::add_constraints(class core::pose::Pose &) –> void

add_evaluation(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) → None

add a PoseEvaluator derived instance for decoy-processing

C++: protocols::abinitio::AbrelaxApplication::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, : pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) → pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication

C++: protocols::abinitio::AbrelaxApplication::operator=(const class protocols::abinitio::AbrelaxApplication &) –> class protocols::abinitio::AbrelaxApplication &

check_filters(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, pose: pyrosetta.rosetta.core.pose.Pose) → bool

check if the given pose passes the set of abinitio filters.

C++: protocols::abinitio::AbrelaxApplication::check_filters(class core::pose::Pose &) –> bool

close_loops(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str) → bool

return pose with simple fold-tree that has small <0.1 RMSD to input pose

C++: protocols::abinitio::AbrelaxApplication::close_loops(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, const class std::basic_string<char> &) –> bool

do_distributed_rerun(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) → None

run process_decoy on all poses in silent-in file – use of JobDistributor

C++: protocols::abinitio::AbrelaxApplication::do_distributed_rerun() –> void

do_rerun(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) → None

run process_decoy on all poses in silent-in file

C++: protocols::abinitio::AbrelaxApplication::do_rerun() –> void

fold(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, extended_pose: pyrosetta.rosetta.core.pose.Pose, prot_ptr: protocols::abinitio::Protocol) → None

run abrelax-type protocols

C++: protocols::abinitio::AbrelaxApplication::fold(class core::pose::Pose &, class std::shared_ptr<class protocols::abinitio::Protocol>) –> void

multi_fast_relax(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, abinitio_protocol: protocols::abinitio::Protocol, : pyrosetta.rosetta.core.scoring.ScoreFunction, jobdist: pyrosetta.rosetta.protocols.jobdist.PlainSilentFileJobDistributor, curr_nstruct: int, curr_job: protocols::jobdist::BasicJob) → bool

relax multiple structures that are stored in abinitio_protocol.structure_store

C++: protocols::abinitio::AbrelaxApplication::multi_fast_relax(class protocols::abinitio::Protocol &, class std::shared_ptr<class core::scoring::ScoreFunction>, class protocols::jobdist::PlainSilentFileJobDistributor, int &, class std::shared_ptr<class protocols::jobdist::BasicJob> &) –> bool

process_decoy(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str, : pyrosetta.rosetta.core.io.silent.SilentStruct) → None

diagnostic stuff, i.e., computing numbers like an RMSD for each decoy and storing in silent-score-file

put everything in here. — actually it mainly calls the evaluator_->apply method. add diagnostic stuff either here as explicit code or in form of a PoseEvaluator to evaluator_ ( see setup () ) the latter has the advantage that the specific evaluation can be carried out during the run of the protocol e.g., for abinitio:debug ( output to stage1_outfile stage2_outfile… )

C++: protocols::abinitio::AbrelaxApplication::process_decoy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::basic_string<char>, class core::io::silent::SilentStruct &) const –> void

register_options() → None

C++: protocols::abinitio::AbrelaxApplication::register_options() –> void

relax(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, tag: str) → None

relax structure ( fast / classic as controlled by cmd-options )

C++: protocols::abinitio::AbrelaxApplication::relax(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, const class std::basic_string<char> &) –> void

run(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) → None

run application code: calls do_rerun() or fold() depending on cmd-options

C++: protocols::abinitio::AbrelaxApplication::run() –> void

setup(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication) → None

initialization of application: read some pdb files, set evaluator_

C++: protocols::abinitio::AbrelaxApplication::setup() –> void

setup_fold(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, extended_pose: pyrosetta.rosetta.core.pose.Pose, prot_ptr: protocols::abinitio::Protocol) → None

setup everything needed for fold() — calls helper functions below

C++: protocols::abinitio::AbrelaxApplication::setup_fold(class core::pose::Pose &, class std::shared_ptr<class protocols::abinitio::Protocol> &) –> void

class pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged

Bases: pyrosetta.rosetta.protocols.moves.PoseCondition

(helper) functor class which keeps track of initial phi/psi values.

calls of operator ( pose ) compare the initial phi/psi values

/to the current values of the given pose. Returns false once all phi/psi values

have been modified.

__call__(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::abinitio::AllResiduesChanged::operator()(const class core::pose::Pose &) –> bool

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose, insert_map: pyrosetta.rosetta.utility.vector1_unsigned_long, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose) -> None
3. __init__(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, arg0: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

assign(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, : pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged) → pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged

C++: protocols::abinitio::AllResiduesChanged::operator=(const class protocols::abinitio::AllResiduesChanged &) –> class protocols::abinitio::AllResiduesChanged &

show_unmoved(self: pyrosetta.rosetta.protocols.abinitio.AllResiduesChanged, pose: pyrosetta.rosetta.core.pose.Pose, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::abinitio::AllResiduesChanged::show_unmoved(const class core::pose::Pose &, class std::basic_ostream<char> &) –> void

pyrosetta.rosetta.protocols.abinitio.Broker_main() → None

Initiates AbrelaxMover using the job distribution (jd2)

C++: protocols::abinitio::Broker_main() –> void

class pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio

Bases: pyrosetta.rosetta.protocols.abinitio.Protocol

@ detail general usage: ClassicAbinitio abinitio; abinitio.init( pose ); … while(nstruct) { abinitio.apply( pose ); }

call ClassicAbinitio::register_options() before core::init::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

• Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on.

Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.

• Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch

and runs for 2000 cycles.

• Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions

is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.

• Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for

finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() …

Behaviour can be changed in the following ways:

use non-classic FragmentMover –> eg. not uniformly sampled fragments, but using some weighting –> large and small moves doesn’t have to be 3mers and 9mers… use other movers… —> or other fragets for the “convenience constructor” use custom trial classes –> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves …

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover, : int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, fragset_small: pyrosetta.rosetta.core.fragment.FragSet, fragset_large: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, arg0: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) → None

C++: protocols::abinitio::Protocol::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void

apply(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::ClassicAbinitio::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.Protocol, : pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.abinitio.Protocol

C++: protocols::abinitio::Protocol::operator=(const class protocols::abinitio::Protocol &) –> class protocols::abinitio::Protocol &

bQuickTest(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → bool

C++: protocols::abinitio::ClassicAbinitio::bQuickTest() const –> bool

brute_move_large(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::brute_move_large() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

brute_move_small(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::brute_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::centroid_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.abinitio.ClassicAbinitio) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::ClassicAbinitio::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>

evaluate_pose(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: protocols::abinitio::Protocol::evaluate_pose(class core::pose::Pose &, class std::basic_string<char>, class core::io::silent::SilentStruct &) const –> void

evaluator(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator

C++: protocols::abinitio::Protocol::evaluator() –> class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>

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>

fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::fullatom_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.

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

get_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::abinitio::Protocol::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.abinitio.ClassicAbinitio) → str

C++: protocols::abinitio::ClassicAbinitio::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.abinitio.ClassicAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::ClassicAbinitio::init(const class core::pose::Pose &) –> void

just_smooth_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → bool

C++: protocols::abinitio::ClassicAbinitio::just_smooth_cycles() const –> bool

kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.abinitio.KinematicControl

C++: protocols::abinitio::Protocol::kinematics() –> const class protocols::abinitio::KinematicControl &

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

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

mc(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::moves::MonteCarlo

C++: protocols::abinitio::ClassicAbinitio::mc() –> class protocols::moves::MonteCarlo &

movemap(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::abinitio::ClassicAbinitio::movemap() –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

output_debug_structure(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None

C++: protocols::abinitio::Protocol::output_debug_structure(class core::pose::Pose &, class std::basic_string<char>) –> void

register_options() → None

C++: protocols::abinitio::ClassicAbinitio::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

return_centroid(*args, **kwargs)

Overloaded function.

1. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) -> bool

C++: protocols::abinitio::Protocol::return_centroid() const –> bool

2. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) -> None

C++: protocols::abinitio::Protocol::return_centroid(bool) –> void

set_centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_centroid_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_cycles(*args, **kwargs)

Overloaded function.

1. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) -> None
2. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles: float) -> None

C++: protocols::abinitio::ClassicAbinitio::set_cycles(double) –> void

set_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::abinitio::Protocol::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> void

set_fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_fullatom_scorefxn(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_kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol, kc: pyrosetta.rosetta.protocols.abinitio.KinematicControl) → None

C++: protocols::abinitio::Protocol::set_kinematics(class std::shared_ptr<class protocols::abinitio::KinematicControl>) –> void

set_mc(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : protocols::moves::MonteCarlo) → None

C++: protocols::abinitio::ClassicAbinitio::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::abinitio::ClassicAbinitio::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_moves(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover) → None

C++: protocols::abinitio::ClassicAbinitio::set_moves(class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> 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_weight(*args, **kwargs)

Overloaded function.

1. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float) -> None
2. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float, stage: pyrosetta.rosetta.protocols.abinitio.StageID) -> None

C++: protocols::abinitio::ClassicAbinitio::set_score_weight(enum core::scoring::ScoreType, double, enum protocols::abinitio::ClassicAbinitio::StageID) –> void

set_silentout_file_name(self: pyrosetta.rosetta.protocols.abinitio.Protocol, str: str) → None

C++: protocols::abinitio::Protocol::set_silentout_file_name(class std::basic_string<char>) –> void

set_skip_stage1(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, setting: bool) → None

C++: protocols::abinitio::ClassicAbinitio::set_skip_stage1(bool) –> void

set_skip_stage2(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, setting: bool) → None

C++: protocols::abinitio::ClassicAbinitio::set_skip_stage2(bool) –> void

set_stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new: int) → None

C++: protocols::abinitio::ClassicAbinitio::set_stage4_cycles(unsigned long) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

smooth_move_small(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::smooth_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

stage1_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage1_cycles() const –> unsigned long

stage2_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage2_cycles() const –> unsigned long

stage3_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage3_cycles() const –> unsigned long

stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage4_cycles() const –> unsigned long

stage5_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage5_cycles() const –> unsigned long

start_from_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → bool

C++: protocols::abinitio::Protocol::start_from_centroid() const –> bool

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

total_trials(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::total_trials() const –> unsigned long

type(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler

Bases: pyrosetta.rosetta.protocols.abinitio.FragmentSampler

@ detail general usage: ConstraintFragmentSampler abinitio; abinitio.init( pose ); … while(nstruct) { abinitio.apply( pose ); }

call ConstraintFragmentSampler::register_options() before core::init::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

• Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on.

Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.

• Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch

and runs for 2000 cycles.

• Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions

is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.

• Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for

finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() …

Behaviour can be changed in the following ways:

use non-classic FragmentMover –> eg. not uniformly sampled fragments, but using some weighting –> large and small moves doesn’t have to be 3mers and 9mers… use other movers… —> or other fragets for the “convenience constructor” use custom trial classes –> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves …

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler, broker: protocols::topology_broker::TopologyBroker) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler, arg0: pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::ConstraintFragmentSampler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler, : pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler) → pyrosetta.rosetta.protocols.abinitio.ConstraintFragmentSampler

C++: protocols::abinitio::ConstraintFragmentSampler::operator=(const class protocols::abinitio::ConstraintFragmentSampler &) –> class protocols::abinitio::ConstraintFragmentSampler &

bQuickTest(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → bool

C++: protocols::abinitio::FragmentSampler::bQuickTest() const –> bool

check_loops(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::abinitio::FragmentSampler::check_loops(class core::pose::Pose &) –> bool

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.abinitio.ConstraintFragmentSampler) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::ConstraintFragmentSampler::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>

current_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::FragmentSampler::current_scorefxn() const –> const class core::scoring::ScoreFunction &

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.

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

get_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::abinitio::FragmentSampler::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.abinitio.ConstraintFragmentSampler) → str

C++: protocols::abinitio::ConstraintFragmentSampler::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 > > &

just_smooth_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → bool

C++: protocols::abinitio::FragmentSampler::just_smooth_cycles() const –> bool

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

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

name() → str

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

register_options() → None

C++: protocols::abinitio::ConstraintFragmentSampler::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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_cycles(*args, **kwargs)

Overloaded function.

1. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) -> None
2. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, increase_cycles: float) -> None

C++: protocols::abinitio::FragmentSampler::set_cycles(double) –> 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_score_weight(*args, **kwargs)

Overloaded function.

1. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float) -> None
2. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float, stage: pyrosetta.rosetta.protocols.abinitio.StageID) -> None

C++: protocols::abinitio::FragmentSampler::set_score_weight(enum core::scoring::ScoreType, double, enum protocols::abinitio::StageID) –> void

set_stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, stage4_cycles_new: int) → None

C++: protocols::abinitio::FragmentSampler::set_stage4_cycles(unsigned long) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

stage1_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage1_cycles() const –> unsigned long

stage2_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage2_cycles() const –> unsigned long

stage3_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage3_cycles() const –> unsigned long

stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage4_cycles() const –> unsigned long

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

topology_broker(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, set: protocols::topology_broker::TopologyBroker) → None

C++: protocols::abinitio::FragmentSampler::topology_broker(class std::shared_ptr<class protocols::topology_broker::TopologyBroker>) –> void

type(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.abinitio.DomainAssembly

Bases: pyrosetta.rosetta.protocols.moves.Mover

insert fragments in a linker region. Very similar to what’s in looprelax_main

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.DomainAssembly) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.DomainAssembly, linker_start: int, linker_end: int, fragset_large: pyrosetta.rosetta.core.fragment.FragSet, fragset_small: pyrosetta.rosetta.core.fragment.FragSet) -> None
3. __init__(self: pyrosetta.rosetta.protocols.abinitio.DomainAssembly, arg0: pyrosetta.rosetta.protocols.abinitio.DomainAssembly) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.abinitio.DomainAssembly, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::DomainAssembly::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.DomainAssembly, : pyrosetta.rosetta.protocols.abinitio.DomainAssembly) → pyrosetta.rosetta.protocols.abinitio.DomainAssembly

C++: protocols::abinitio::DomainAssembly::operator=(const class protocols::abinitio::DomainAssembly &) –> class protocols::abinitio::DomainAssembly &

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.abinitio.DomainAssembly) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::DomainAssembly::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.abinitio.DomainAssembly) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::DomainAssembly::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.

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.abinitio.DomainAssembly) → str

C++: protocols::abinitio::DomainAssembly::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

mover_name() → str

C++: protocols::abinitio::DomainAssembly::mover_name() –> std::string

name() → str

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

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

C++: protocols::abinitio::DomainAssembly::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.abinitio.FoldConstraints

Bases: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio

extension of ClassicAbinitio Protocol to adapt the folding process for the presence of distance constraints

Main Function: switch distance constraints based on distance in the FoldTree ( i.e., in sequence for simple FoldTrees )

This is achieved by replacing the pose’s ConstraintSet with the special purpose class MaxSeqSepConstraintSet the latter class will only score constraints that are sufficiently close in FoldTree/Sequence ( as controlled by the threshold with set_max_seq_sep() ) the protocol ranks up the max_seq_sep parameter while folding proceeds through the stages. to this extend it overloads methods prepare_stageX() do_stage1_cycles()

the other substantial difference to ClassicAbinitio is that minimizations are carried out. method min_trial() is called each time the max_seq_sep is changed. ( inhibit: -no_minimize )

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover, dummy: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, fragset3mer: pyrosetta.rosetta.core.fragment.FragSet, fragset9mer: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, arg0: pyrosetta.rosetta.protocols.abinitio.FoldConstraints) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) → None

C++: protocols::abinitio::Protocol::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void

apply(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, pose: pyrosetta.rosetta.core.pose.Pose) → None

run the protocol

C++: protocols::abinitio::FoldConstraints::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.Protocol, : pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.abinitio.Protocol

C++: protocols::abinitio::Protocol::operator=(const class protocols::abinitio::Protocol &) –> class protocols::abinitio::Protocol &

bQuickTest(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → bool

C++: protocols::abinitio::ClassicAbinitio::bQuickTest() const –> bool

brute_move_large(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::brute_move_large() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

brute_move_small(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::brute_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::centroid_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.abinitio.FoldConstraints) → pyrosetta.rosetta.protocols.moves.Mover

…

C++: protocols::abinitio::FoldConstraints::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>

evaluate_pose(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: protocols::abinitio::Protocol::evaluate_pose(class core::pose::Pose &, class std::basic_string<char>, class core::io::silent::SilentStruct &) const –> void

evaluator(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator

C++: protocols::abinitio::Protocol::evaluator() –> class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>

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>

fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::fullatom_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.

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

get_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::abinitio::Protocol::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.abinitio.FoldConstraints) → str

C++: protocols::abinitio::FoldConstraints::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.abinitio.ClassicAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::ClassicAbinitio::init(const class core::pose::Pose &) –> void

just_smooth_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → bool

C++: protocols::abinitio::ClassicAbinitio::just_smooth_cycles() const –> bool

kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.abinitio.KinematicControl

C++: protocols::abinitio::Protocol::kinematics() –> const class protocols::abinitio::KinematicControl &

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

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

mc(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::moves::MonteCarlo

C++: protocols::abinitio::ClassicAbinitio::mc() –> class protocols::moves::MonteCarlo &

movemap(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::abinitio::ClassicAbinitio::movemap() –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

output_debug_structure(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None

C++: protocols::abinitio::Protocol::output_debug_structure(class core::pose::Pose &, class std::basic_string<char>) –> void

register_options() → None

C++: protocols::abinitio::FoldConstraints::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

return_centroid(*args, **kwargs)

Overloaded function.

1. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) -> bool

C++: protocols::abinitio::Protocol::return_centroid() const –> bool

2. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) -> None

C++: protocols::abinitio::Protocol::return_centroid(bool) –> void

set_centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_centroid_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_constraint_weight(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, setting: float) → None

C++: protocols::abinitio::FoldConstraints::set_constraint_weight(double) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_cycles(*args, **kwargs)

Overloaded function.

1. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) -> None
2. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, increase_cycles: float) -> None

C++: protocols::abinitio::ClassicAbinitio::set_cycles(double) –> void

set_default_options(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints) → None

C++: protocols::abinitio::FoldConstraints::set_default_options() –> void

set_default_scores(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints) → None

sets the usual scores ( score0,score1, score2/5 etc. ) and additionally atom_pair_constraints to 1.0

C++: protocols::abinitio::FoldConstraints::set_default_scores() –> void

set_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::abinitio::Protocol::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> void

set_fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_fullatom_scorefxn(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_kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol, kc: pyrosetta.rosetta.protocols.abinitio.KinematicControl) → None

C++: protocols::abinitio::Protocol::set_kinematics(class std::shared_ptr<class protocols::abinitio::KinematicControl>) –> void

set_mc(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : protocols::moves::MonteCarlo) → None

C++: protocols::abinitio::ClassicAbinitio::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::abinitio::ClassicAbinitio::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_moves(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover) → None

C++: protocols::abinitio::ClassicAbinitio::set_moves(class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> 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_weight(*args, **kwargs)

Overloaded function.

1. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float) -> None
2. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float, stage: pyrosetta.rosetta.protocols.abinitio.StageID) -> None

C++: protocols::abinitio::ClassicAbinitio::set_score_weight(enum core::scoring::ScoreType, double, enum protocols::abinitio::ClassicAbinitio::StageID) –> void

set_show_viol_level(self: pyrosetta.rosetta.protocols.abinitio.FoldConstraints, setting: int) → None

C++: protocols::abinitio::FoldConstraints::set_show_viol_level(unsigned long) –> void

set_silentout_file_name(self: pyrosetta.rosetta.protocols.abinitio.Protocol, str: str) → None

C++: protocols::abinitio::Protocol::set_silentout_file_name(class std::basic_string<char>) –> void

set_skip_stage1(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, setting: bool) → None

C++: protocols::abinitio::ClassicAbinitio::set_skip_stage1(bool) –> void

set_skip_stage2(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, setting: bool) → None

C++: protocols::abinitio::ClassicAbinitio::set_skip_stage2(bool) –> void

set_stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio, stage4_cycles_new: int) → None

C++: protocols::abinitio::ClassicAbinitio::set_stage4_cycles(unsigned long) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

smooth_move_small(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::ClassicAbinitio::smooth_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

stage1_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage1_cycles() const –> unsigned long

stage2_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage2_cycles() const –> unsigned long

stage3_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage3_cycles() const –> unsigned long

stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage4_cycles() const –> unsigned long

stage5_cycles(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::stage5_cycles() const –> unsigned long

start_from_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → bool

C++: protocols::abinitio::Protocol::start_from_centroid() const –> bool

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

total_trials(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) → int

C++: protocols::abinitio::ClassicAbinitio::total_trials() const –> unsigned long

type(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.abinitio.FragmentSampler

Bases: pyrosetta.rosetta.protocols.moves.Mover

@ detail general usage: FragmentSampler abinitio; abinitio.init( pose ); … while(nstruct) { abinitio.apply( pose ); }

call FragmentSampler::register_options() before core::init::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

• Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on.

Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.

• Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch

and runs for 2000 cycles.

• Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions

is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.

• Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for

finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() …

Behaviour can be changed in the following ways:

use non-classic FragmentMover –> eg. not uniformly sampled fragments, but using some weighting –> large and small moves doesn’t have to be 3mers and 9mers… use other movers… —> or other fragets for the “convenience constructor” use custom trial classes –> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves …

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, broker: protocols::topology_broker::TopologyBroker) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, arg0: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

apply(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::FragmentSampler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, : pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → pyrosetta.rosetta.protocols.abinitio.FragmentSampler

C++: protocols::abinitio::FragmentSampler::operator=(const class protocols::abinitio::FragmentSampler &) –> class protocols::abinitio::FragmentSampler &

bQuickTest(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → bool

C++: protocols::abinitio::FragmentSampler::bQuickTest() const –> bool

check_loops(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::abinitio::FragmentSampler::check_loops(class core::pose::Pose &) –> bool

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.abinitio.FragmentSampler) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::FragmentSampler::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>

current_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::FragmentSampler::current_scorefxn() const –> const class core::scoring::ScoreFunction &

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.

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

get_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::abinitio::FragmentSampler::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.abinitio.FragmentSampler) → str

C++: protocols::abinitio::FragmentSampler::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 > > &

just_smooth_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → bool

C++: protocols::abinitio::FragmentSampler::just_smooth_cycles() const –> bool

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

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

name() → str

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

register_options() → None

C++: protocols::abinitio::FragmentSampler::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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_cycles(*args, **kwargs)

Overloaded function.

1. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) -> None
2. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, increase_cycles: float) -> None

C++: protocols::abinitio::FragmentSampler::set_cycles(double) –> 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_score_weight(*args, **kwargs)

Overloaded function.

1. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float) -> None
2. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float, stage: pyrosetta.rosetta.protocols.abinitio.StageID) -> None

C++: protocols::abinitio::FragmentSampler::set_score_weight(enum core::scoring::ScoreType, double, enum protocols::abinitio::StageID) –> void

set_stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, stage4_cycles_new: int) → None

C++: protocols::abinitio::FragmentSampler::set_stage4_cycles(unsigned long) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

stage1_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage1_cycles() const –> unsigned long

stage2_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage2_cycles() const –> unsigned long

stage3_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage3_cycles() const –> unsigned long

stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler) → int

C++: protocols::abinitio::FragmentSampler::stage4_cycles() const –> unsigned long

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

topology_broker(self: pyrosetta.rosetta.protocols.abinitio.FragmentSampler, set: protocols::topology_broker::TopologyBroker) → None

C++: protocols::abinitio::FragmentSampler::topology_broker(class std::shared_ptr<class protocols::topology_broker::TopologyBroker>) –> void

type(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio

Bases: pyrosetta.rosetta.protocols.abinitio.Protocol

@ detail general usage: MembraneAbinitio abinitio; abinitio.init( pose ); … while(nstruct) { abinitio.apply( pose ); }

call MembraneAbinitio::register_options() before core::init::init to add relevant options to the applications help

, with the following stages, all of which uses a different ScoreFunction based on the cen_std.wts in minirosetta_database:

• Stage 1: large (usually 9mer) randomly selected fragment insertions, only VDW term turned on.

Uses score0.wts_patch and runs for either a maximum of 2000 cycles or until all moveable phi/psi values have been changed.

• Stage 2: large randomly selected fragment insertions, more score terms turned on. Uses score1.wts_patch

and runs for 2000 cycles.

• Stage 3: uses large randomly selected fragment insertions, although the size of the fragment insertions

is tunable via the set_apply_large_frags( bool ) method. Alternates between score2.wts_patch and score5.wts_patch, running tunable numbers of 2000-cycle iterations between the two scoring functions.

• Stage 4: uses small (usually 3mer) fragment insertions with the fragment selection based on the Gunn cost for

finding local fragment moves. Runs for 4000-cycles and uses score3.wts_patch.

The class implements the basic abinito approach as known from rosetta++. We tried to set this up, such that behaviour of the protocol can be changed in many different ways ( see, e.g., FoldConstraints ). To be able to change the behaviour of the protocol easily the class-apply function and methods called therein (e.g., prepare_XXX() / do_XXX_cycles() ) should not directly change moves or trials. A reference to the currently used score-function should be obtained by mc().score_function() …

Behaviour can be changed in the following ways:

use non-classic FragmentMover –> eg. not uniformly sampled fragments, but using some weighting –> large and small moves doesn’t have to be 3mers and 9mers… use other movers… —> or other fragets for the “convenience constructor” use custom trial classes –> overload update_moves()

change sampling behaviour: overload prepare_XXX() methods: these are called before the cycling for a certain stage begins overload do_stageX_cycles() : the actual loops over trial-moves …

change scoring functions: overload set_default_scores() weight-changes effective for all stages: set_score_weight()

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_small_top25: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover, : int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, fragset_small: pyrosetta.rosetta.core.fragment.FragSet, fragset_small_top25: pyrosetta.rosetta.core.fragment.FragSet, fragset_large: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, arg0: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) -> None

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

add_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) → None

C++: protocols::abinitio::Protocol::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void

add_spanning_region(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::MembraneAbinitio::add_spanning_region(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::MembraneAbinitio::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, : pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio

C++: protocols::abinitio::MembraneAbinitio::operator=(const class protocols::abinitio::MembraneAbinitio &) –> class protocols::abinitio::MembraneAbinitio &

bQuickTest(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → bool

C++: protocols::abinitio::MembraneAbinitio::bQuickTest() const –> bool

brute_move_large(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::MembraneAbinitio::brute_move_large() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

brute_move_small(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::MembraneAbinitio::brute_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

brute_move_small_top25(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::MembraneAbinitio::brute_move_small_top25() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::centroid_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

checkpoint(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose, id: str) → None

C++: protocols::abinitio::MembraneAbinitio::checkpoint(class core::pose::Pose &, const class std::basic_string<char> &) –> void

clear_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → None

C++: protocols::abinitio::MembraneAbinitio::clear_checkpoints() –> void

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

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

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::abinitio::MembraneAbinitio::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>

evaluate_pose(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) → None

C++: protocols::abinitio::Protocol::evaluate_pose(class core::pose::Pose &, class std::basic_string<char>, class core::io::silent::SilentStruct &) const –> void

evaluator(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator

C++: protocols::abinitio::Protocol::evaluator() –> class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>

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>

fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::abinitio::Protocol::fullatom_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.

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

get_checkpoints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.checkpoint.CheckPointer

C++: protocols::abinitio::Protocol::get_checkpoints() –> class protocols::checkpoint::CheckPointer &

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.abinitio.MembraneAbinitio) → str

C++: protocols::abinitio::MembraneAbinitio::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.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::MembraneAbinitio::init(const class core::pose::Pose &) –> void

just_smooth_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → bool

C++: protocols::abinitio::MembraneAbinitio::just_smooth_cycles() const –> bool

kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → pyrosetta.rosetta.protocols.abinitio.KinematicControl

C++: protocols::abinitio::Protocol::kinematics() –> const class protocols::abinitio::KinematicControl &

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

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

mc(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → pyrosetta.rosetta.protocols.moves.MonteCarlo

C++: protocols::abinitio::MembraneAbinitio::mc() –> class protocols::moves::MonteCarlo &

move_all_inserted(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::MembraneAbinitio::move_all_inserted(class core::pose::Pose &) –> void

movemap(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::abinitio::MembraneAbinitio::movemap() –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

output_debug_structure(self: pyrosetta.rosetta.protocols.abinitio.Protocol, pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → None

C++: protocols::abinitio::Protocol::output_debug_structure(class core::pose::Pose &, class std::basic_string<char>) –> void

print_debug(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::abinitio::MembraneAbinitio::print_debug(class core::pose::Pose &) –> void

recover_checkpoint(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, pose: pyrosetta.rosetta.core.pose.Pose, id: str) → bool

C++: protocols::abinitio::MembraneAbinitio::recover_checkpoint(class core::pose::Pose &, const class std::basic_string<char> &) –> bool

register_options() → None

C++: protocols::abinitio::MembraneAbinitio::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

return_centroid(*args, **kwargs)

Overloaded function.

1. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) -> bool

C++: protocols::abinitio::Protocol::return_centroid() const –> bool

2. return_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) -> None

C++: protocols::abinitio::Protocol::return_centroid(bool) –> void

set_centroid_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_centroid_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_cycles(*args, **kwargs)

Overloaded function.

1. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) -> None
2. set_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, increase_cycles: float) -> None

C++: protocols::abinitio::MembraneAbinitio::set_cycles(double) –> void

set_evaluation(self: pyrosetta.rosetta.protocols.abinitio.Protocol, ev: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::abinitio::Protocol::set_evaluation(class std::shared_ptr<class protocols::evaluation::MetaPoseEvaluator>) –> void

set_fullatom_scorefxn(self: pyrosetta.rosetta.protocols.abinitio.Protocol, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::abinitio::Protocol::set_fullatom_scorefxn(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_kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol, kc: pyrosetta.rosetta.protocols.abinitio.KinematicControl) → None

C++: protocols::abinitio::Protocol::set_kinematics(class std::shared_ptr<class protocols::abinitio::KinematicControl>) –> void

set_mc(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, : pyrosetta.rosetta.protocols.moves.MonteCarlo) → None

C++: protocols::abinitio::MembraneAbinitio::set_mc(class std::shared_ptr<class protocols::moves::MonteCarlo>) –> void

set_movemap(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::abinitio::MembraneAbinitio::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

set_moves(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, brute_move_small: protocols::simple_moves::FragmentMover, brute_move_large: protocols::simple_moves::FragmentMover, smooth_move_small: protocols::simple_moves::FragmentMover) → None

C++: protocols::abinitio::MembraneAbinitio::set_moves(class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>, class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> 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_only_stage4(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, value: bool) → None

C++: protocols::abinitio::MembraneAbinitio::set_only_stage4(bool) –> void

set_score_weight(*args, **kwargs)

Overloaded function.

1. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float) -> None
2. set_score_weight(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, : pyrosetta.rosetta.core.scoring.ScoreType, setting: float, stage: pyrosetta.rosetta.protocols.abinitio.StageID) -> None

C++: protocols::abinitio::MembraneAbinitio::set_score_weight(enum core::scoring::ScoreType, double, enum protocols::abinitio::MembraneAbinitio::StageID) –> void

set_silentout_file_name(self: pyrosetta.rosetta.protocols.abinitio.Protocol, str: str) → None

C++: protocols::abinitio::Protocol::set_silentout_file_name(class std::basic_string<char>) –> void

set_stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio, stage4_cycles_new: int) → None

C++: protocols::abinitio::MembraneAbinitio::set_stage4_cycles(unsigned long) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) const –> void

smooth_move_small(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → protocols::simple_moves::FragmentMover

C++: protocols::abinitio::MembraneAbinitio::smooth_move_small() –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

stage1_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → int

C++: protocols::abinitio::MembraneAbinitio::stage1_cycles() const –> unsigned long

stage2_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → int

C++: protocols::abinitio::MembraneAbinitio::stage2_cycles() const –> unsigned long

stage3_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → int

C++: protocols::abinitio::MembraneAbinitio::stage3_cycles() const –> unsigned long

stage4_cycles(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → int

C++: protocols::abinitio::MembraneAbinitio::stage4_cycles() const –> unsigned long

start_from_centroid(self: pyrosetta.rosetta.protocols.abinitio.Protocol) → bool

C++: protocols::abinitio::Protocol::start_from_centroid() const –> bool

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

total_trials(self: pyrosetta.rosetta.protocols.abinitio.MembraneAbinitio) → int

C++: protocols::abinitio::MembraneAbinitio::total_trials() const –> unsigned long

type(*args, **kwargs)

Overloaded function.

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

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.abinitio.hash_value(*args, **kwargs)

Overloaded function.

1. hash_value(val: pyrosetta.rosetta.protocols.abinitio.PairingStatEntry) -> int

C++: protocols::abinitio::hash_value(const class protocols::abinitio::PairingStatEntry &) –> unsigned long

2. hash_value(val: pyrosetta.rosetta.core.scoring.dssp.StrandPairing) -> int

C++: protocols::abinitio::hash_value(const class core::scoring::dssp::StrandPairing &) –> unsigned long

pyrosetta.rosetta.protocols.abinitio.register_common_options() → None

C++: protocols::abinitio::register_common_options() –> void

pyrosetta.rosetta.protocols.abinitio.register_options_broker() → None

Registers options that are relevant to the application. This function

must be called prior to Broker_main() or Loopbuild_Threading_main().

C++: protocols::abinitio::register_options_broker() –> void

pyrosetta.rosetta.protocols.abinitio.run_boinc_debug() → int

C++: protocols::abinitio::run_boinc_debug() –> int