abinitio

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.

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 std::string &) –> 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 &, std::string, class core::io::silent::SilentStruct &) const –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, citation_list: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Get citation information for the AbinitioRelaxApplication.

Includes trRosetta information if this is set.

Vikram K. Mulligan (vmulligan.org).

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

static 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 std::string &) –> 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

set_use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxApplication, setting: bool) None

Set whether we’re using trRosetta.

Vikram K. Mulligan (vmulligan.org).

C++: protocols::abinitio::AbrelaxApplication::set_use_trRosetta_constraints(const bool) –> 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.AbrelaxMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

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

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

assign(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, : pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) pyrosetta.rosetta.protocols.abinitio.AbrelaxMover

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

clear(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) None

C++: protocols::abinitio::AbrelaxMover::clear() –> 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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

closure_protocol(*args, **kwargs)

Overloaded function.

  1. closure_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) -> protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure

C++: protocols::abinitio::AbrelaxMover::closure_protocol() –> class std::shared_ptr<class protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure>

  1. closure_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, set: protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure) -> None

C++: protocols::abinitio::AbrelaxMover::closure_protocol(class std::shared_ptr<class protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure>) –> void

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.AbrelaxMover) pyrosetta.rosetta.protocols.moves.Mover

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

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

fpd

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

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) str

C++: protocols::abinitio::AbrelaxMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() str

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

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

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

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

post_loop_closure_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, move: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::abinitio::AbrelaxMover::post_loop_closure_protocol(class std::shared_ptr<class protocols::moves::Mover>) –> void

pre_loop_closure_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, move: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::abinitio::AbrelaxMover::pre_loop_closure_protocol(class std::shared_ptr<class protocols::moves::Mover>) –> void

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

relax_protocol(*args, **kwargs)

Overloaded function.

  1. relax_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) -> protocols::relax::RelaxProtocolBase

C++: protocols::abinitio::AbrelaxMover::relax_protocol() –> class std::shared_ptr<class protocols::relax::RelaxProtocolBase>

  1. relax_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, set: protocols::relax::RelaxProtocolBase) -> None

C++: protocols::abinitio::AbrelaxMover::relax_protocol(class std::shared_ptr<class protocols::relax::RelaxProtocolBase>) –> void

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

sampling_protocol(*args, **kwargs)

Overloaded function.

  1. sampling_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) -> protocols::abinitio::FragmentSampler

C++: protocols::abinitio::AbrelaxMover::sampling_protocol() –> class std::shared_ptr<class protocols::abinitio::FragmentSampler>

  1. sampling_protocol(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover, set: protocols::abinitio::FragmentSampler) -> None

C++: protocols::abinitio::AbrelaxMover::sampling_protocol(class std::shared_ptr<class protocols::abinitio::FragmentSampler>) –> void

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

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

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

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

set_defaults(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) None

C++: protocols::abinitio::AbrelaxMover::set_defaults() –> void

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

topology_broker(self: pyrosetta.rosetta.protocols.abinitio.AbrelaxMover) protocols::topology_broker::TopologyBroker

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.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.

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 &, std::ostream &) –> void

class pyrosetta.rosetta.protocols.abinitio.AlternativePairings

Bases: pybind11_builtins.pybind11_object

add_pairing(self: pyrosetta.rosetta.protocols.abinitio.AlternativePairings, : pyrosetta.rosetta.protocols.abinitio.PairingStatEntry) bool

C++: protocols::abinitio::AlternativePairings::add_pairing(const class protocols::abinitio::PairingStatEntry &) –> bool

antiparallel(self: pyrosetta.rosetta.protocols.abinitio.AlternativePairings) bool

C++: protocols::abinitio::AlternativePairings::antiparallel() const –> bool

build_constraints(self: pyrosetta.rosetta.protocols.abinitio.AlternativePairings, pose: pyrosetta.rosetta.core.pose.Pose, cst: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) None

C++: protocols::abinitio::AlternativePairings::build_constraints(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &) const –> void

compatible(self: pyrosetta.rosetta.protocols.abinitio.AlternativePairings, pairing: pyrosetta.rosetta.core.scoring.dssp.StrandPairing) bool

C++: protocols::abinitio::AlternativePairings::compatible(const class core::scoring::dssp::StrandPairing &) const –> bool

show(self: pyrosetta.rosetta.protocols.abinitio.AlternativePairings, : pyrosetta.rosetta.std.ostream) None

C++: protocols::abinitio::AlternativePairings::show(std::ostream &) const –> 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()

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
class StageID

Bases: pybind11_builtins.pybind11_object

Members:

ALL_STAGES

STAGE_1

STAGE_2

STAGE_3a

STAGE_3b

STAGE_4

STAGE_4rot

STAGE_5

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
property name
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

property bSkipStage1_
property bSkipStage2_
property bSkipStage3_
property bSkipStage4_
property bSkipStage5_
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 &, std::string, 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.

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

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

get_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) 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>

static 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 &, std::string) –> void

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

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

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

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

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

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

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

property recover_low_stages_
static 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

  1. 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

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

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

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

set_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: 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.ClassicAbinitio.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(std::string) –> 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

Set the ‘type’ string

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

set_use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) None

Set whether we’re using trRosetta constraints.

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

supports_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) bool
This overrides the default and indicates that the ClassicAbInitio protocol DOES support

trRosetta constraints.

C++: protocols::abinitio::ClassicAbinitio::supports_trRosetta_constraints() 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) bool

Get whether we’re using trRosetta constraints.

Vikram K. Mulligan (vmulligan.org).

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

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()

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.

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

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

get_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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

set_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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC

Bases: pyrosetta.rosetta.protocols.abinitio.KinematicControl

add_chainbreak_variants(*args, **kwargs)

Overloaded function.

  1. add_chainbreak_variants(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, pose: pyrosetta.rosetta.core.pose.Pose) -> None

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

  1. add_chainbreak_variants(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, pose: pyrosetta.rosetta.core.pose.Pose, max_dist: int, : pyrosetta.rosetta.core.kinematics.ShortestPathInFoldTree) -> None

C++: protocols::abinitio::KinematicControl::add_chainbreak_variants(class core::pose::Pose &, unsigned long, const class core::kinematics::ShortestPathInFoldTree &) const –> void

add_score_weights(self: pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC, : pyrosetta.rosetta.core.scoring.ScoreFunction, progress: float) None

C++: protocols::abinitio::CoordinateConstraintKC::add_score_weights(class core::scoring::ScoreFunction &, double) const –> void

assign(self: pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC, : pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC) pyrosetta.rosetta.protocols.abinitio.CoordinateConstraintKC

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

final_fold_tree(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl) pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::abinitio::KinematicControl::final_fold_tree() const –> const class core::kinematics::FoldTree &

jump_mover(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl) protocols::simple_moves::FragmentMover

C++: protocols::abinitio::KinematicControl::jump_mover() const –> class std::shared_ptr<class protocols::simple_moves::FragmentMover>

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

C++: protocols::abinitio::KinematicControl::movemap() const –> const class core::kinematics::MoveMap &

movemap_ptr(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl) pyrosetta.rosetta.core.kinematics.MoveMap

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

prepare_pose_for_sampling(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, pose: pyrosetta.rosetta.core.pose.Pose) bool

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

sampling_fold_tree(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl) pyrosetta.rosetta.core.kinematics.FoldTree

C++: protocols::abinitio::KinematicControl::sampling_fold_tree() const –> const class core::kinematics::FoldTree &

set_final_fold_tree(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, f: pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::abinitio::KinematicControl::set_final_fold_tree(const class core::kinematics::FoldTree &) –> void

set_jump_mover(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, jm: protocols::simple_moves::FragmentMover) None

C++: protocols::abinitio::KinematicControl::set_jump_mover(class std::shared_ptr<class protocols::simple_moves::FragmentMover>) –> void

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

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

set_sampling_fold_tree(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, f: pyrosetta.rosetta.core.kinematics.FoldTree) None

C++: protocols::abinitio::KinematicControl::set_sampling_fold_tree(const class core::kinematics::FoldTree &) –> void

set_strict_movemap(self: pyrosetta.rosetta.protocols.abinitio.KinematicControl, mm: pyrosetta.rosetta.core.kinematics.MoveMap) None

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

get_name(self: pyrosetta.rosetta.protocols.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

static mover_name() str

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

static name() str

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

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

each use.

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

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator, : pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator) pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator

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

create_mover(self: pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator) str

C++: protocols::abinitio::DomainAssemblyCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.abinitio.DomainAssemblyCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio

Bases: pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst

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.KinematicTaskControl, pose: pyrosetta.rosetta.core.pose.Pose) None

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

assign(self: pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio, : pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio) pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio

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

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.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

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

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

current_kinematics(self: pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl) protocols::abinitio::KinematicControl

C++: protocols::abinitio::KinematicTaskControl::current_kinematics() –> class std::shared_ptr<class protocols::abinitio::KinematicControl>

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 &, std::string, 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.

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

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

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

C++: protocols::abinitio::KinematicTaskControl::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.DoubleLayerKinematicAbinitio) str

C++: protocols::abinitio::DoubleLayerKinematicAbinitio::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.KinematicTaskControl, pose: pyrosetta.rosetta.core.pose.Pose) None

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

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

static name() str

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

new_kinematics(self: pyrosetta.rosetta.protocols.abinitio.DoubleLayerKinematicAbinitio, pose: pyrosetta.rosetta.core.pose.Pose) protocols::abinitio::KinematicControl

C++: protocols::abinitio::DoubleLayerKinematicAbinitio::new_kinematics(class core::pose::Pose &) –> class std::shared_ptr<class protocols::abinitio::KinematicControl>

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 &, std::string) –> void

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

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

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

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

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

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

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

static register_options() None

C++: protocols::abinitio::Protocol::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

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

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

sampling_protocol(self: pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl) pyrosetta.rosetta.protocols.abinitio.Protocol

C++: protocols::abinitio::KinematicTaskControl::sampling_protocol() –> class std::shared_ptr<class protocols::abinitio::Protocol>

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_coord_cst_weight_array(self: pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst, vec: pyrosetta.rosetta.utility.vector1_double) None

C++: protocols::abinitio::LoopJumpFoldCst::set_coord_cst_weight_array(const class utility::vector1<double, class std::allocator<double> > &) –> void

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

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

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

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

set_dump_weights_file(self: pyrosetta.rosetta.protocols.abinitio.LoopJumpFoldCst, str: str) None

C++: protocols::abinitio::LoopJumpFoldCst::set_dump_weights_file(const std::string &) –> 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_input_pose_is_fa(*args, **kwargs)

Overloaded function.

  1. set_input_pose_is_fa(self: pyrosetta.rosetta.protocols.abinitio.KinematicTaskControl) -> None

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

C++: protocols::abinitio::KinematicTaskControl::set_input_pose_is_fa(bool) –> void

set_kinematics(self: pyrosetta.rosetta.protocols.abinitio.Protocol, kc: protocols::abinitio::KinematicControl) None

C++: protocols::abinitio::Protocol::set_kinematics(class std::shared_ptr<class protocols::abinitio::KinematicControl>) –> 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_silentout_file_name(self: pyrosetta.rosetta.protocols.abinitio.Protocol, str: str) None

C++: protocols::abinitio::Protocol::set_silentout_file_name(std::string) –> void

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

Set the ‘type’ string

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

set_use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) None

Set whether we’re using trRosetta constraints.

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

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

supports_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) bool
Report whether this protocol supports trRosetta constraints. The base

class returns false; derived classes can override this and return true.

C++: protocols::abinitio::Protocol::supports_trRosetta_constraints() 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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) bool

Get whether we’re using trRosetta constraints.

Vikram K. Mulligan (vmulligan.org).

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

class pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup

Bases: pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup

assign(self: pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup, : pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup) pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup

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

clean_jumps(self: pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::abinitio::TemplateJumpSetup::clean_jumps(const class protocols::jumping::JumpSample &) const –> class protocols::jumping::JumpSample

create_jump_sample(self: pyrosetta.rosetta.protocols.abinitio.FixTemplateJumpSetup) pyrosetta.rosetta.protocols.jumping.JumpSample

C++: protocols::abinitio::FixTemplateJumpSetup::create_jump_sample() const –> class protocols::jumping::JumpSample

generate_jump_frags(self: pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup, : pyrosetta.rosetta.protocols.jumping.JumpSample, : pyrosetta.rosetta.core.kinematics.MoveMap) pyrosetta.rosetta.core.fragment.FragSet
returns an ordered FragSet that is compatible with the JumpSample

default: generate jumps from ss-library according to JumpSample

C++: protocols::abinitio::TemplateJumpSetup::generate_jump_frags(const class protocols::jumping::JumpSample &, const class core::kinematics::MoveMap &) const –> class std::shared_ptr<class core::fragment::FragSet>

is_helix_jump(self: pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup, p: pyrosetta.rosetta.core.scoring.dssp.Pairing) bool

C++: protocols::abinitio::TemplateJumpSetup::is_helix_jump(const class core::scoring::dssp::Pairing &) const –> bool

type_name(self: pyrosetta.rosetta.protocols.abinitio.TemplateJumpSetup) str

C++: protocols::abinitio::TemplateJumpSetup::type_name() const –> std::string

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 )

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
class StageID

Bases: pybind11_builtins.pybind11_object

Members:

ALL_STAGES

STAGE_1

STAGE_2

STAGE_3a

STAGE_3b

STAGE_4

STAGE_4rot

STAGE_5

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
property name
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

property bSkipStage1_
property bSkipStage2_
property bSkipStage3_
property bSkipStage4_
property bSkipStage5_
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 &, std::string, 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.

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

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

get_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) 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>

static 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 &, std::string) –> void

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

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

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

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

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

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

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

property recover_low_stages_
static 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

  1. 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

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

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

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

set_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: 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.ClassicAbinitio.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(std::string) –> 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

Set the ‘type’ string

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

set_use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol, setting: bool) None

Set whether we’re using trRosetta constraints.

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

supports_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.ClassicAbinitio) bool
This overrides the default and indicates that the ClassicAbInitio protocol DOES support

trRosetta constraints.

C++: protocols::abinitio::ClassicAbinitio::supports_trRosetta_constraints() 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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_trRosetta_constraints(self: pyrosetta.rosetta.protocols.abinitio.Protocol) bool

Get whether we’re using trRosetta constraints.

Vikram K. Mulligan (vmulligan.org).

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

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()

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.

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

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

get_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

static name() str

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

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

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

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

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

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

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

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

static register_options() None

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

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

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

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

set_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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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, type_in: str) -> None

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.abinitio.HedgeArchive

Bases: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive

accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, : pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, batch: protocols::jd2::archive::Batch) bool

C++: protocols::abinitio::HedgeArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

  1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

  2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, batch: protocols::jd2::archive::Batch) bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::EvaluatedArchive::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, : pyrosetta.rosetta.protocols.abinitio.HedgeArchive) pyrosetta.rosetta.protocols.abinitio.HedgeArchive

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

collect(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, batch: protocols::jd2::archive::Batch, : pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::abinitio::HedgeArchive::collect(const class protocols::jd2::archive::Batch &, class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) const –> void

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::finished() const –> bool

generate_batch(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive) None

C++: protocols::abinitio::HedgeArchive::generate_batch() –> void

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

called when nothing is happening

C++: protocols::jd2::archive::ArchiveBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, : pyrosetta.rosetta.core.io.silent.SilentFileData) None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::abinitio::HedgeArchive::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

initialize(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) None

only overloaded this to add some verbosity each time we read structures

C++: protocols::jd2::archive::EvaluatedArchive::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

static register_options() None

Archive specific options

C++: protocols::jd2::archive::EvaluatedArchive::register_options() –> void

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive) None

C++: protocols::abinitio::HedgeArchive::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::EvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, : pyrosetta.rosetta.std.istream) None

C++: protocols::abinitio::HedgeArchive::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.abinitio.HedgeArchive, : pyrosetta.rosetta.std.ostream) None

save and restore status of archive to file-system

C++: protocols::abinitio::HedgeArchive::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

  1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) -> None

  2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::EvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, col: str) float

C++: protocols::jd2::archive::EvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) None
set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

set common evaluators: eg. ConstraintEvaluator if -cst_file is present

C++: protocols::jd2::archive::EvaluatedArchive::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, : protocols::jd2::archive::Batch) bool
old-batches might be outdated and should not be computed anymore

return true for this query if this is the case for old_batch

C++: protocols::jd2::archive::AbstractArchiveBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax

Bases: pyrosetta.rosetta.protocols.abinitio.IterativeBase

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
class IterationStage

Bases: pybind11_builtins.pybind11_object

Members:

ENUMERATION

TOPO_RESAMPLING

PURE_TOPO_RESAMPLING

STAGE2_RESAMPLING

NOESY_PHASEII_TOPO

NOESY_PHASEII_S2_RESAMPLING

CEN2FULLATOM

LAST_CENTROID_START

RIGID_CORE_RESAMPLING

FINISHED

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
property name
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

  1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

  2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

overloaded to handel special convergence check ‘pool_converged_rmsd’

add structure to Archive.. return false if structure is rejected.

C++: protocols::abinitio::IterativeBase::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, : pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax

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

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

determine_score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

determine variation of scores (those that are non-zeros in select_weights_ )

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations() const –> bool

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) bool

C++: protocols::abinitio::IterativeAbrelax::finished() const –> bool

gen_diversity_pool(*args, **kwargs)

Overloaded function.

  1. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch) -> None

  2. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch, fullatom: bool) -> None

C++: protocols::abinitio::IterativeBase::gen_diversity_pool(class protocols::jd2::archive::Batch &, bool) –> void

gen_dynamic_patches(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) None

C++: protocols::abinitio::IterativeBase::gen_dynamic_patches(class protocols::jd2::archive::Batch &) –> void

gen_evaluation_output(*args, **kwargs)

Overloaded function.

  1. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) -> None

  2. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch, fullatom: bool) -> None

generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy

note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys

C++: protocols::abinitio::IterativeBase::gen_evaluation_output(class protocols::jd2::archive::Batch &, bool) –> void

generate_batch(*args, **kwargs)

Overloaded function.

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) -> None

C++: protocols::abinitio::IterativeAbrelax::generate_batch() –> void

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, : protocols::jd2::archive::Batch, repeat_id: int) -> int

C++: protocols::abinitio::IterativeAbrelax::generate_batch(class protocols::jd2::archive::Batch &, unsigned long) –> unsigned long

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) None

C++: protocols::abinitio::IterativeAbrelax::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, : pyrosetta.rosetta.core.io.silent.SilentFileData) None

C++: protocols::abinitio::IterativeAbrelax::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

init_from_options(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options() –> void

initialize(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) None

C++: protocols::abinitio::IterativeAbrelax::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) None

C++: protocols::abinitio::IterativeAbrelax::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

ready_for_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

we are always ready to generate a new batch

C++: protocols::abinitio::IterativeBase::ready_for_batch() const –> bool

static register_options() None

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

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

C++: protocols::abinitio::IterativeBase::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) bool

C++: protocols::abinitio::IterativeAbrelax::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.istream) None

C++: protocols::abinitio::IterativeBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, : pyrosetta.rosetta.std.ostream) None

C++: protocols::abinitio::IterativeAbrelax::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

  1. save_to_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax) -> None

  2. save_to_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, suffix: str) -> None

C++: protocols::abinitio::IterativeAbrelax::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col: str) float

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_finish_stage(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, setting: pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage) None

where to stop ?

C++: protocols::abinitio::IterativeBase::set_finish_stage(enum protocols::abinitio::IterativeBase::IterationStage) –> void

set_manager(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, manager: protocols::jd2::archive::BaseArchiveManager) None

C++: protocols::abinitio::IterativeAbrelax::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) None
set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

setup JumpNrEvaluator

C++: protocols::abinitio::IterativeBase::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.abinitio.IterativeAbrelax, batch: protocols::jd2::archive::Batch) bool

C++: protocols::abinitio::IterativeAbrelax::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

test_for_stage_end(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

calls increment_stage() if appropriate

C++: protocols::abinitio::IterativeBase::test_for_stage_end() –> void

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

update_noesy_filter_files(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, current: str, fullatom: bool) None

C++: protocols::abinitio::IterativeBase::update_noesy_filter_files(const std::string &, bool) –> void

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.abinitio.IterativeBase

Bases: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
class IterationStage

Bases: pybind11_builtins.pybind11_object

Members:

ENUMERATION

TOPO_RESAMPLING

PURE_TOPO_RESAMPLING

STAGE2_RESAMPLING

NOESY_PHASEII_TOPO

NOESY_PHASEII_S2_RESAMPLING

CEN2FULLATOM

LAST_CENTROID_START

RIGID_CORE_RESAMPLING

FINISHED

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
property name
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

  1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

  2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

overloaded to handel special convergence check ‘pool_converged_rmsd’

add structure to Archive.. return false if structure is rejected.

C++: protocols::abinitio::IterativeBase::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.protocols.abinitio.IterativeBase) pyrosetta.rosetta.protocols.abinitio.IterativeBase

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

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

determine_score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

determine variation of scores (those that are non-zeros in select_weights_ )

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations() const –> bool

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

archive is finished when at last stage

C++: protocols::abinitio::IterativeBase::finished() const –> bool

gen_diversity_pool(*args, **kwargs)

Overloaded function.

  1. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch) -> None

  2. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch, fullatom: bool) -> None

C++: protocols::abinitio::IterativeBase::gen_diversity_pool(class protocols::jd2::archive::Batch &, bool) –> void

gen_dynamic_patches(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) None

C++: protocols::abinitio::IterativeBase::gen_dynamic_patches(class protocols::jd2::archive::Batch &) –> void

gen_evaluation_output(*args, **kwargs)

Overloaded function.

  1. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) -> None

  2. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch, fullatom: bool) -> None

generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy

note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys

C++: protocols::abinitio::IterativeBase::gen_evaluation_output(class protocols::jd2::archive::Batch &, bool) –> void

generate_batch(*args, **kwargs)

Overloaded function.

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) -> None

generate a new batch, use different recipe according to current stage

C++: protocols::abinitio::IterativeBase::generate_batch() –> void

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch, repeat_id: int) -> int

C++: protocols::abinitio::IterativeBase::generate_batch(class protocols::jd2::archive::Batch &, unsigned long) –> unsigned long

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

while waiting for jobs to finish

C++: protocols::abinitio::IterativeBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::abinitio::IterativeBase::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

init_from_options(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options() –> void

initialize(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

do initializing work that requires fully setup object here

C++: protocols::abinitio::IterativeBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) None

overloaded so we can test for end of IterationStage after reading

C++: protocols::abinitio::IterativeBase::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

ready_for_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

we are always ready to generate a new batch

C++: protocols::abinitio::IterativeBase::ready_for_batch() const –> bool

static register_options() None

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

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

C++: protocols::abinitio::IterativeBase::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.istream) None

C++: protocols::abinitio::IterativeBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::abinitio::IterativeBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

  1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> None

  2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col: str) float

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_finish_stage(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, setting: pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage) None

where to stop ?

C++: protocols::abinitio::IterativeBase::set_finish_stage(enum protocols::abinitio::IterativeBase::IterationStage) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) None
set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

setup JumpNrEvaluator

C++: protocols::abinitio::IterativeBase::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) bool

we are not interested in batches that were generated in old stages

C++: protocols::abinitio::IterativeBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

test_for_stage_end(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

calls increment_stage() if appropriate

C++: protocols::abinitio::IterativeBase::test_for_stage_end() –> void

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

update_noesy_filter_files(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, current: str, fullatom: bool) None

C++: protocols::abinitio::IterativeBase::update_noesy_filter_files(const std::string &, bool) –> void

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.abinitio.IterativeCentroid

Bases: pyrosetta.rosetta.protocols.abinitio.IterativeBase

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
class IterationStage

Bases: pybind11_builtins.pybind11_object

Members:

ENUMERATION

TOPO_RESAMPLING

PURE_TOPO_RESAMPLING

STAGE2_RESAMPLING

NOESY_PHASEII_TOPO

NOESY_PHASEII_S2_RESAMPLING

CEN2FULLATOM

LAST_CENTROID_START

RIGID_CORE_RESAMPLING

FINISHED

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
property name
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

  1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

  2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

overloaded to handel special convergence check ‘pool_converged_rmsd’

add structure to Archive.. return false if structure is rejected.

C++: protocols::abinitio::IterativeBase::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid, : pyrosetta.rosetta.protocols.abinitio.IterativeCentroid) pyrosetta.rosetta.protocols.abinitio.IterativeCentroid

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

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

determine_score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

determine variation of scores (those that are non-zeros in select_weights_ )

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations() const –> bool

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

archive is finished when at last stage

C++: protocols::abinitio::IterativeBase::finished() const –> bool

gen_diversity_pool(*args, **kwargs)

Overloaded function.

  1. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid, batch: protocols::jd2::archive::Batch) -> None

  2. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid, batch: protocols::jd2::archive::Batch, fullatom: bool) -> None

C++: protocols::abinitio::IterativeCentroid::gen_diversity_pool(class protocols::jd2::archive::Batch &, bool) –> void

gen_dynamic_patches(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) None

C++: protocols::abinitio::IterativeBase::gen_dynamic_patches(class protocols::jd2::archive::Batch &) –> void

gen_evaluation_output(*args, **kwargs)

Overloaded function.

  1. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) -> None

  2. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch, fullatom: bool) -> None

generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy

note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys

C++: protocols::abinitio::IterativeBase::gen_evaluation_output(class protocols::jd2::archive::Batch &, bool) –> void

generate_batch(*args, **kwargs)

Overloaded function.

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) -> None

generate a new batch, use different recipe according to current stage

C++: protocols::abinitio::IterativeBase::generate_batch() –> void

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch, repeat_id: int) -> int

C++: protocols::abinitio::IterativeBase::generate_batch(class protocols::jd2::archive::Batch &, unsigned long) –> unsigned long

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

while waiting for jobs to finish

C++: protocols::abinitio::IterativeBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::abinitio::IterativeBase::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

init_from_options(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options() –> void

initialize(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

do initializing work that requires fully setup object here

C++: protocols::abinitio::IterativeBase::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) None

overloaded so we can test for end of IterationStage after reading

C++: protocols::abinitio::IterativeBase::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

ready_for_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

we are always ready to generate a new batch

C++: protocols::abinitio::IterativeBase::ready_for_batch() const –> bool

static register_options() None

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

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

C++: protocols::abinitio::IterativeBase::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid) bool

C++: protocols::abinitio::IterativeCentroid::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.istream) None

C++: protocols::abinitio::IterativeBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::abinitio::IterativeBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

  1. save_to_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid) -> None

  2. save_to_file(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid, suffix: str) -> None

save and restore archive to file-system

C++: protocols::abinitio::IterativeCentroid::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col: str) float

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_finish_stage(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, setting: pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage) None

where to stop ?

C++: protocols::abinitio::IterativeBase::set_finish_stage(enum protocols::abinitio::IterativeBase::IterationStage) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) None
set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

setup JumpNrEvaluator

C++: protocols::abinitio::IterativeBase::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) bool

we are not interested in batches that were generated in old stages

C++: protocols::abinitio::IterativeBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

test_for_stage_end(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

calls increment_stage() if appropriate

C++: protocols::abinitio::IterativeBase::test_for_stage_end() –> void

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

update_noesy_filter_files(self: pyrosetta.rosetta.protocols.abinitio.IterativeCentroid, current: str, fullatom: bool) None

C++: protocols::abinitio::IterativeCentroid::update_noesy_filter_files(const std::string &, bool) –> void

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.abinitio.IterativeFullatom

Bases: pyrosetta.rosetta.protocols.abinitio.IterativeBase

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
class IterationStage

Bases: pybind11_builtins.pybind11_object

Members:

ENUMERATION

TOPO_RESAMPLING

PURE_TOPO_RESAMPLING

STAGE2_RESAMPLING

NOESY_PHASEII_TOPO

NOESY_PHASEII_S2_RESAMPLING

CEN2FULLATOM

LAST_CENTROID_START

RIGID_CORE_RESAMPLING

FINISHED

CEN2FULLATOM = <IterationStage.CEN2FULLATOM: 7>
ENUMERATION = <IterationStage.ENUMERATION: 1>
FINISHED = <IterationStage.FINISHED: 9>
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
property name
LAST_CENTROID_START = <IterationStage.CEN2FULLATOM: 7>
NOESY_PHASEII_S2_RESAMPLING = <IterationStage.NOESY_PHASEII_S2_RESAMPLING: 6>
NOESY_PHASEII_TOPO = <IterationStage.NOESY_PHASEII_TOPO: 5>
PURE_TOPO_RESAMPLING = <IterationStage.PURE_TOPO_RESAMPLING: 3>
RIGID_CORE_RESAMPLING = <IterationStage.RIGID_CORE_RESAMPLING: 8>
STAGE2_RESAMPLING = <IterationStage.STAGE2_RESAMPLING: 4>
TOPO_RESAMPLING = <IterationStage.TOPO_RESAMPLING: 2>
accepts_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

—- methods to keep statistics of acceptance

C++: protocols::jd2::archive::ArchiveBase::accepts_since_last_batch() –> unsigned long &

add_evaluated_structure(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

add decoy to Archive

evaluate decoy and call add_evaluated_structure

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::add_evaluated_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

add_evaluation(*args, **kwargs)

Overloaded function.

  1. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) -> None

  2. add_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator, weight: float) -> None

add new PoseEvaluation to set of evaluators, specify weight for contribution to select_score()

C++: protocols::jd2::archive::EvaluatedArchive::add_evaluation(class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, double) –> void

add_structure(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, new_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, alternative_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct, : protocols::jd2::archive::Batch) bool

overloaded to handel special convergence check ‘pool_converged_rmsd’

add structure to Archive.. return false if structure is rejected.

C++: protocols::abinitio::IterativeBase::add_structure(class std::shared_ptr<class core::io::silent::SilentStruct>, class std::shared_ptr<class core::io::silent::SilentStruct>, const class protocols::jd2::archive::Batch &) –> bool

assign(self: pyrosetta.rosetta.protocols.abinitio.IterativeFullatom, : pyrosetta.rosetta.protocols.abinitio.IterativeFullatom) pyrosetta.rosetta.protocols.abinitio.IterativeFullatom

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

current_acceptance_ratio(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) float

C++: protocols::jd2::archive::ArchiveBase::current_acceptance_ratio() const –> double

decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::jd2::archive::ArchiveBase::decoys() –> class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

determine_score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

determine variation of scores (those that are non-zeros in select_weights_ )

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::determine_score_variations() const –> bool

evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) bool

specify if decoys are evaluated on the master or (non-local i.e., on the individual slave nodes)

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_local() const –> bool

evaluate_silent_struct(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, from_batch: pyrosetta.rosetta.core.io.silent.SilentStruct) pyrosetta.rosetta.core.io.silent.SilentStruct

yields an “evaluated” silent-struct which can be queried with select_score

will run scoring-process if evaluate_local() otherwise just returns the intpu-silent-struct

C++: protocols::jd2::archive::EvaluatedArchive::evaluate_silent_struct(class std::shared_ptr<class core::io::silent::SilentStruct>) const –> class std::shared_ptr<class core::io::silent::SilentStruct>

evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t

C++: protocols::jd2::archive::EvaluatedArchive::evaluators() const –> const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &

finished(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) bool

archive is finished when at last stage

C++: protocols::abinitio::IterativeBase::finished() const –> bool

gen_diversity_pool(*args, **kwargs)

Overloaded function.

  1. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch) -> None

  2. gen_diversity_pool(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : protocols::jd2::archive::Batch, fullatom: bool) -> None

C++: protocols::abinitio::IterativeBase::gen_diversity_pool(class protocols::jd2::archive::Batch &, bool) –> void

gen_dynamic_patches(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) None

C++: protocols::abinitio::IterativeBase::gen_dynamic_patches(class protocols::jd2::archive::Batch &) –> void

gen_evaluation_output(*args, **kwargs)

Overloaded function.

  1. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) -> None

  2. gen_evaluation_output(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch, fullatom: bool) -> None

generate flags and stuff for the out-sourced evaluation —> such that score_final column is returned for each decoy

note needs to be public, since IterativeCentroid calls this from IterativeFullatom to prepare evaluation for soon to be full-atom decoys

C++: protocols::abinitio::IterativeBase::gen_evaluation_output(class protocols::jd2::archive::Batch &, bool) –> void

generate_batch(*args, **kwargs)

Overloaded function.

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeFullatom) -> None

C++: protocols::abinitio::IterativeFullatom::generate_batch() –> void

  1. generate_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeFullatom, : protocols::jd2::archive::Batch, repeat_id: int) -> int

C++: protocols::abinitio::IterativeFullatom::generate_batch(class protocols::jd2::archive::Batch &, unsigned long) –> unsigned long

get_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) float

C++: protocols::jd2::archive::EvaluatedArchive::get_weight(const std::string &) const –> double

has_evaluator(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) bool

is a certain elvaluator present ?

C++: protocols::jd2::archive::EvaluatedArchive::has_evaluator(const std::string &) –> bool

idle(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

while waiting for jobs to finish

C++: protocols::abinitio::IterativeBase::idle() –> void

init_from_decoy_set(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) None

overloaded to make input decoys appear the same as decoys coming from batches

C++: protocols::abinitio::IterativeBase::init_from_decoy_set(const class core::io::silent::SilentFileData &) –> void

init_from_options(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) None

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::init_from_options() –> void

initialize(self: pyrosetta.rosetta.protocols.abinitio.IterativeFullatom) None

do initializing work that requires fully setup object here

C++: protocols::abinitio::IterativeFullatom::initialize() –> void

load_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, filename: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

C++: protocols::jd2::archive::ArchiveBase::load_decoys(const std::string &, class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) protocols::jd2::archive::BaseArchiveManager

access to the ArchiveManager (control of batches)

C++: protocols::jd2::archive::AbstractArchiveBase::manager() –> class protocols::jd2::archive::BaseArchiveManager &

name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase) str

C++: protocols::jd2::archive::AbstractArchiveBase::name() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

how many structures should be in archive .. varies from decoys().size() in startup phase.

C++: protocols::jd2::archive::ArchiveBase::nstruct() const –> unsigned long

proposed_since_last_batch(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::proposed_since_last_batch() const –> unsigned long

read_structures(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData, alternative_decoys: pyrosetta.rosetta.core.io.silent.SilentFileData, batch: protocols::jd2::archive::Batch) None

overloaded so we can test for end of IterationStage after reading

C++: protocols::abinitio::IterativeBase::read_structures(class core::io::silent::SilentFileData &, class core::io::silent::SilentFileData &, const class protocols::jd2::archive::Batch &) –> void

ready_for_batch(self: pyrosetta.rosetta.protocols.abinitio.IterativeFullatom) bool

C++: protocols::abinitio::IterativeFullatom::ready_for_batch() const –> bool

static register_options() None

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

remove_evaluation(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str) None

remove Evaluator

C++: protocols::jd2::archive::EvaluatedArchive::remove_evaluation(const std::string &) –> void

rescore(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

C++: protocols::abinitio::IterativeBase::rescore() –> void

reset_accept_counter(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) None

C++: protocols::jd2::archive::ArchiveBase::reset_accept_counter() –> void

restore_from_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) bool

overloaded that we can sort the pool after reading

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::restore_from_file() –> bool

restore_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.istream) None

C++: protocols::abinitio::IterativeBase::restore_status(std::istream &) –> void

save_decoys(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, dirname: str, name: str, decoys: pyrosetta.rosetta.std.list_std_shared_ptr_core_io_silent_SilentStruct_std_allocator_std_shared_ptr_core_io_silent_SilentStruct_t) None

helper routine to save decoys properly

C++: protocols::jd2::archive::ArchiveBase::save_decoys(const std::string &, const std::string &, const class std::list<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &) –> void

save_status(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, : pyrosetta.rosetta.std.ostream) None

C++: protocols::abinitio::IterativeBase::save_status(std::ostream &) const –> void

save_to_file(*args, **kwargs)

Overloaded function.

  1. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) -> None

  2. save_to_file(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, suffix: str) -> None

overloaded to save / restore the variance_archive_

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::save_to_file(std::string) –> void

score_variation(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive, col: str) float

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variation(const std::string &) const –> double

score_variations(self: pyrosetta.rosetta.protocols.jd2.archive.NormalizedEvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::NormalizedEvaluatedArchive::score_variations() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::jd2::archive::EvaluatedArchive::scorefxn() const –> const class core::scoring::ScoreFunction &

select_score(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, evaluated_decoy: pyrosetta.rosetta.core.io.silent.SilentStruct) float

compute score according to select_weights — this can contain any evaluator columns

C++: protocols::jd2::archive::EvaluatedArchive::select_score(class std::shared_ptr<class core::io::silent::SilentStruct>) –> double

set_evaluate_local(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: bool) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluate_local(bool) –> void

set_evaluators(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_const_protocols_evaluation_PoseEvaluator_t, : pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_evaluators(const class std::map<std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<const class protocols::evaluation::PoseEvaluator> > > > &, const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

set_finish_stage(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, setting: pyrosetta.rosetta.protocols.abinitio.IterativeBase.IterationStage) None

where to stop ?

C++: protocols::abinitio::IterativeBase::set_finish_stage(enum protocols::abinitio::IterativeBase::IterationStage) –> void

set_manager(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, manager: protocols::jd2::archive::BaseArchiveManager) None

C++: protocols::jd2::archive::AbstractArchiveBase::set_manager(class protocols::jd2::archive::BaseArchiveManager *) –> void

set_name(self: pyrosetta.rosetta.protocols.jd2.archive.AbstractArchiveBase, set: str) None

set name of archive ( used also for save_to_file and restore_from_file )

C++: protocols::jd2::archive::AbstractArchiveBase::set_name(const std::string &) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase, set: int) None

set target size of pool

C++: protocols::jd2::archive::ArchiveBase::set_nstruct(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, scorefxn_: pyrosetta.rosetta.core.scoring.ScoreFunction) None

set scorefxn used for evaluation

C++: protocols::jd2::archive::EvaluatedArchive::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_weight(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, column: str, weight: float) None
set weight of an evaluator or a column otherwise present in silent-structs

(i.e, score, chainbreak, external evaluation like score_final )

C++: protocols::jd2::archive::EvaluatedArchive::set_weight(const std::string &, double) –> void

set_weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive, setting: pyrosetta.rosetta.std.map_std_string_double) None

C++: protocols::jd2::archive::EvaluatedArchive::set_weights(const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &) –> void

setup_default_evaluators(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

setup JumpNrEvaluator

C++: protocols::abinitio::IterativeBase::setup_default_evaluators() –> void

start_evaluation_timer(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) None

C++: protocols::jd2::archive::EvaluatedArchive::start_evaluation_timer() const –> void

statistics_valid(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) bool

C++: protocols::jd2::archive::ArchiveBase::statistics_valid() –> bool

still_interested(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, batch: protocols::jd2::archive::Batch) bool

we are not interested in batches that were generated in old stages

C++: protocols::abinitio::IterativeBase::still_interested(const class protocols::jd2::archive::Batch &) const –> bool

test_for_stage_end(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase) None

calls increment_stage() if appropriate

C++: protocols::abinitio::IterativeBase::test_for_stage_end() –> void

total_accepts(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_accepts() –> unsigned long

total_proposed(self: pyrosetta.rosetta.protocols.jd2.archive.ArchiveBase) int

C++: protocols::jd2::archive::ArchiveBase::total_proposed() –> unsigned long

update_noesy_filter_files(self: pyrosetta.rosetta.protocols.abinitio.IterativeBase, current: str, fullatom: bool) None

C++: protocols::abinitio::IterativeBase::update_noesy_filter_files(const std::string &, bool) –> void

weights(self: pyrosetta.rosetta.protocols.jd2.archive.EvaluatedArchive) pyrosetta.rosetta.std.map_std_string_double

C++: protocols::jd2::archive::EvaluatedArchive::weights() const –> const class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &

class pyrosetta.rosetta.protocols.abinitio.JumpingFoldConstraintsWrapper

Bases: pyrosetta.rosetta.protocols.abinitio.KinematicAbinitio

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
class StageID

Bases: pybind11_builtins.pybind11_object

Members:

ALL_STAGES

STAGE_1

STAGE_2

STAGE_3a

STAGE_3b

STAGE_4

STAGE_4rot

STAGE_5

ALL_STAGES = <StageID.ALL_STAGES: 0>
STAGE_1 = <StageID.STAGE_1: 1>
STAGE_2 = <StageID.STAGE_2: 2>
STAGE_3a = <StageID.STAGE_3a: 3>
STAGE_3b = <StageID.STAGE_3b: 4>
STAGE_4 = <StageID.STAGE_4: 5>
STAGE_4rot = <StageID.STAGE_4rot: 6>
STAGE_5 = <StageID.STAGE_5: 7>
property name
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.JumpingFoldConstraintsWrapper, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::abinitio::JumpingFoldConstraintsWrapper::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

property bSkipStage1_
property bSkipStage2_
property bSkipStage3_
property bSkipStage4_
property bSkipStage5_
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: