components

Bindings for protocols::forge::components namespace

class pyrosetta.rosetta.protocols.forge.components.BDR

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_instruction(*args, **kwargs)

Overloaded function.

  1. add_instruction(self: pyrosetta.rosetta.protocols.forge.components.BDR, bi: pyrosetta.rosetta.protocols.forge.build.BuildInstruction) -> None

  2. add_instruction(self: pyrosetta.rosetta.protocols.forge.components.BDR, bi: pyrosetta.rosetta.protocols.forge.build.BuildInstruction, aa_during_design_refine: str) -> None

add instruction to the manager of this BDR (no copy)

BuildInstruction

The allowed amino acid sequence

during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert

C++: protocols::forge::components::BDR::add_instruction(class std::shared_ptr<class protocols::forge::build::BuildInstruction>, const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.forge.components.BDR, pose: pyrosetta.rosetta.core.pose.Pose) None

apply defined moves to given Pose

C++: protocols::forge::components::BDR::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

centroid_loop_mover_str(*args, **kwargs)

Overloaded function.

  1. centroid_loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> str

the loop mover string to use during centroid build

(default “RemodelLoopMover”)

set to either a string the create_loop_mover() LoopMoverFactory

recognizes or the “RemodelLoopMover”

C++: protocols::forge::components::BDR::centroid_loop_mover_str() const –> const std::string &

  1. centroid_loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.BDR, loop_mover_str: str) -> None

the loop mover string to use during centroid build

set to either a string the create_loop_mover() LoopMoverFactory

recognizes or the “RemodelLoopMover”

C++: protocols::forge::components::BDR::centroid_loop_mover_str(const std::string &) –> void

centroid_scorefunction(*args, **kwargs)

Overloaded function.

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> pyrosetta.rosetta.core.scoring.ScoreFunction

the centroid level score function, default “remodel_cen”

C++: protocols::forge::components::BDR::centroid_scorefunction() const –> const class core::scoring::ScoreFunction &

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the centroid level score function

C++: protocols::forge::components::BDR::centroid_scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. centroid_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the centroid level score function

C++: protocols::forge::components::BDR::centroid_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.forge.components.BDR) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::forge::components::BDR::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>

create_directed_dependency(self: pyrosetta.rosetta.protocols.forge.components.BDR, u: pyrosetta.rosetta.protocols.forge.build.BuildInstruction, v: pyrosetta.rosetta.protocols.forge.build.BuildInstruction) None

create directed dependency between two instructions

C++: protocols::forge::components::BDR::create_directed_dependency(class std::shared_ptr<class protocols::forge::build::BuildInstruction>, class std::shared_ptr<class protocols::forge::build::BuildInstruction>) –> void

dr_cycles(*args, **kwargs)

Overloaded function.

  1. dr_cycles(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> int

the number of design-refine cycles to perform, default 3

C++: protocols::forge::components::BDR::dr_cycles() const –> unsigned long

  1. dr_cycles(self: pyrosetta.rosetta.protocols.forge.components.BDR, cycles: int) -> None

set the number of design-refine cycles to perform

set this to 0 to skip design-refine

C++: protocols::forge::components::BDR::dr_cycles(const unsigned long) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.forge.components.BDR) pyrosetta.rosetta.protocols.moves.Mover

create this type of object

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

fullatom_scorefunction(*args, **kwargs)

Overloaded function.

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> pyrosetta.rosetta.core.scoring.ScoreFunction

the full-atom level score function, default score12

C++: protocols::forge::components::BDR::fullatom_scorefunction() const –> const class core::scoring::ScoreFunction &

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the full-atom level score function

C++: protocols::forge::components::BDR::fullatom_scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. fullatom_scorefunction(self: pyrosetta.rosetta.protocols.forge.components.BDR, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set the full-atom level score function

C++: protocols::forge::components::BDR::fullatom_scorefunction(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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.forge.components.BDR) str

C++: protocols::forge::components::BDR::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static loops_buns_polar_calc_name() str
the name for the loops’ buried unsatisfied polars

calculator

C++: protocols::forge::components::BDR::loops_buns_polar_calc_name() –> std::string

max_linear_chainbreak(*args, **kwargs)

Overloaded function.

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> float

the maximum allowed linear chainbreak (default 0.07)

C++: protocols::forge::components::BDR::max_linear_chainbreak() const –> double

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.BDR, threshold: float) -> None

the maximum allowed linear chainbreak

C++: protocols::forge::components::BDR::max_linear_chainbreak(const double) –> void

static name() str

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

static neighborhood_buns_polar_calc_name() str
the name for the loops’ neighborhood buried unsatisfied polars

calculator

C++: protocols::forge::components::BDR::neighborhood_buns_polar_calc_name() –> std::string

static neighborhood_calc_name() str

the name for the loops’ neighborhood calculator

C++: protocols::forge::components::BDR::neighborhood_calc_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

redesign_loop_neighborhood(*args, **kwargs)

Overloaded function.

  1. redesign_loop_neighborhood(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> bool

redesign the neighborhood around the loop? if false, then just

repacks during the design phase (default true)

C++: protocols::forge::components::BDR::redesign_loop_neighborhood() const –> bool

  1. redesign_loop_neighborhood(self: pyrosetta.rosetta.protocols.forge.components.BDR, flag: bool) -> None

redesign the neighborhood around the loop? if false, then just

repacks during the design phase

C++: protocols::forge::components::BDR::redesign_loop_neighborhood(const bool) –> 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

resfile(*args, **kwargs)

Overloaded function.

  1. resfile(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> str

name of the resfile to use during design-refine; empty string

implies no resfile

C++: protocols::forge::components::BDR::resfile() const –> const std::string &

  1. resfile(self: pyrosetta.rosetta.protocols.forge.components.BDR, filename: str) -> None

name of the resfile to use during design-refine; empty string

implies no resfile

C++: protocols::forge::components::BDR::resfile(const std::string &) –> 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 &

use_fullmer(*args, **kwargs)

Overloaded function.

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> bool

use full-mer fragments when building the loop? (default false)

C++: protocols::forge::components::BDR::use_fullmer() const –> bool

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.BDR, flag: bool) -> None

use full-mer fragments when building the loop?

C++: protocols::forge::components::BDR::use_fullmer(const bool) –> void

use_sequence_bias(*args, **kwargs)

Overloaded function.

  1. use_sequence_bias(self: pyrosetta.rosetta.protocols.forge.components.BDR) -> bool

use sequence biased fragments when building the loop? (default false)

C++: protocols::forge::components::BDR::use_sequence_bias() const –> bool

  1. use_sequence_bias(self: pyrosetta.rosetta.protocols.forge.components.BDR, flag: bool) -> None

use sequence biased fragments when building the loop? (default false)

C++: protocols::forge::components::BDR::use_sequence_bias(const bool) –> void

class pyrosetta.rosetta.protocols.forge.components.VarLengthBuild

Bases: pyrosetta.rosetta.protocols.moves.Mover

Component that performs a protocol for user-specified variable length

remodeling of protein backbone segments.

This bootstrap implementation performs centroid level loop building

using 9,3,1-mer fragments and running a LoopMover with the Remodel ‘remodel_cen’ score function. The default loop mover is the forge RemodelLoopMover. It does not yet handle extensions or continuous replacements. This class is under heavy development, expect many changes to both API and internals.

add_rcg(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, rcg: protocols::forge::remodel::RemodelConstraintGenerator) None

C++: protocols::forge::components::VarLengthBuild::add_rcg(class std::shared_ptr<class protocols::forge::remodel::RemodelConstraintGenerator>) –> void

add_setup_mover(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, mover_in: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::forge::components::VarLengthBuild::add_setup_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

add_user_provided_mover(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, mover_in: pyrosetta.rosetta.protocols.moves.Mover) None

C++: protocols::forge::components::VarLengthBuild::add_user_provided_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

apply(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, pose: pyrosetta.rosetta.core.pose.Pose) None

run protocol on given Pose

if procedure successful, return Pose with modifications and a

sealed fold tree, otherwise return Pose with modifications and the in-progress cut fold tree

Before invoking this function it’s best to make sure

the secondary structure in the Pose is marked via the method that you would prefer, e.g. by Dssp (protocols::jumping::Dssp), by the old Rosetta++ binning method (core::pose::set_ss_from_phipsi) or by external method such as reading in a file.

C++: protocols::forge::components::VarLengthBuild::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

cache_fragments(*args, **kwargs)

Overloaded function.

  1. cache_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

cache fragments after picking? (default true)

If true, will cache fragments and reuse them upon each

apply() call instead of repicking every time.

C++: protocols::forge::components::VarLengthBuild::cache_fragments() const –> bool

  1. cache_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

cache fragments after picking?

If true, will cache fragments and reuse them upon each

apply() call instead of repicking every time.

C++: protocols::forge::components::VarLengthBuild::cache_fragments(const bool) –> void

clear_fragments(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

clear any currently cached fragments

C++: protocols::forge::components::VarLengthBuild::clear_fragments() –> 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

clear_rcgs(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_rcgs() –> void

clear_setup_movers(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_setup_movers() –> void

clear_user_provided_movers(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) None

C++: protocols::forge::components::VarLengthBuild::clear_user_provided_movers() –> void

clone(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::forge::components::VarLengthBuild::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.forge.components.VarLengthBuild) pyrosetta.rosetta.protocols.moves.Mover

create a new instance of this type of object

C++: protocols::forge::components::VarLengthBuild::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.forge.components.VarLengthBuild) str

C++: protocols::forge::components::VarLengthBuild::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

ignore_cmdline_enzdes_cstfile(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) None

C++: protocols::forge::components::VarLengthBuild::ignore_cmdline_enzdes_cstfile(const bool) –> void

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

non-const accessor

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

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

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

loop_mover_fold_tree_constant(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) None

C++: protocols::forge::components::VarLengthBuild::loop_mover_fold_tree_constant(const bool) –> void

loop_mover_str(*args, **kwargs)

Overloaded function.

  1. loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

the string id of the loop mover to use

(default “RemodelLoopMover”)

“RemodelLoopMover” for the forge RemodelLoopMover, otherwise a

string recognized by create_loop_mover() in the “LoopMoverFactory”.

C++: protocols::forge::components::VarLengthBuild::loop_mover_str() const –> const std::string &

  1. loop_mover_str(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

set the loop mover to use via string

use “RemodelLoopMover” for the forge RemodelLoopMover,

otherwise set it to a string recognized by create_loop_mover() in the “LoopMoverFactory”.

C++: protocols::forge::components::VarLengthBuild::loop_mover_str(const std::string &) –> void

manager(*args, **kwargs)

Overloaded function.

  1. manager(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> pyrosetta.rosetta.protocols.forge.build.BuildManager

build manager

C++: protocols::forge::components::VarLengthBuild::manager() const –> const class protocols::forge::build::BuildManager &

  1. manager(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, manager: pyrosetta.rosetta.protocols.forge.build.BuildManager) -> None

set build manager; also clears any cached fragments

C++: protocols::forge::components::VarLengthBuild::manager(const class protocols::forge::build::BuildManager &) –> void

max_linear_chainbreak(*args, **kwargs)

Overloaded function.

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> float

return the highest linear chainbreak score a chainbreak can have

and still be considered closed

default 0.07

C++: protocols::forge::components::VarLengthBuild::max_linear_chainbreak() const –> double

  1. max_linear_chainbreak(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, tol: float) -> None

set the highest linear chainbreak score a chainbreak can have

and still be considered closed

C++: protocols::forge::components::VarLengthBuild::max_linear_chainbreak(const double) –> void

static name() str

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

new_secondary_structure_override(*args, **kwargs)

Overloaded function.

  1. new_secondary_structure_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full sequence string with length corresponding to the new

modified pose used to pick secondary structure biased fragments.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_secondary_structure_override() const –> const std::string &

  1. new_secondary_structure_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

full sequence string with length corresponding to the new

modified pose used to pick secondary structure biased fragments.

String with length equals to the new modified pose.

See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick secondary structure biased fragments without modification. All secondary structure settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_secondary_structure_override(const std::string &) –> void

new_sequence_override(*args, **kwargs)

Overloaded function.

  1. new_sequence_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full amino acid string with length corresponding to the new

modified pose used to pick sequence biased fragments.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_sequence_override() const –> const std::string &

  1. new_sequence_override(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, str: str) -> None

full amino acid string with length corresponding to the new

modified pose used to pick sequence biased fragments.

String with length equals to the new modified pose.

See remarks for help on how to determine this. String is allowed to be empty, in which case it will clear the setting.

IMPORTANT: This is an override! If this string is filled,

it will be used as the string to pick sequence biased fragments without modification. All sequence settings that might be taken from the original Pose or from the BuildInstructions will be ignored. The length of this string must be equal to the length of the NEW modified pose, otherwise the protocol will stop with error – you can use BuildManager::dummy_modify() to help figure things out.

C++: protocols::forge::components::VarLengthBuild::new_sequence_override(const std::string &) –> void

num_fragpick(*args, **kwargs)

Overloaded function.

  1. num_fragpick(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> int

the number of fragments to pick at each position

(default 200)

C++: protocols::forge::components::VarLengthBuild::num_fragpick() const –> unsigned long

  1. num_fragpick(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, num: int) -> None

the number of fragments to pick at each position (default 200)

C++: protocols::forge::components::VarLengthBuild::num_fragpick(const unsigned long) –> void

original_sequence(*args, **kwargs)

Overloaded function.

  1. original_sequence(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> str

full sequence string corresponding to original input pose

used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

C++: protocols::forge::components::VarLengthBuild::original_sequence() –> const std::string &

  1. original_sequence(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, seq: str) -> None

full sequence string corresponding to original input pose

used to pick sequence biased fragments; if empty, sequence bias is not used when picking fragments

C++: protocols::forge::components::VarLengthBuild::original_sequence(const 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

recover_original_on_failure(*args, **kwargs)

Overloaded function.

  1. recover_original_on_failure(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

at the end of apply(), reset the Pose to the original Pose if

mover was not successful? (default true)

C++: protocols::forge::components::VarLengthBuild::recover_original_on_failure() const –> bool

  1. recover_original_on_failure(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

at the end of apply(), reset the Pose to the original Pose if

mover was not successful?

C++: protocols::forge::components::VarLengthBuild::recover_original_on_failure(const bool) –> 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

restart_mode(*args, **kwargs)

Overloaded function.

  1. restart_mode(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

Flag to turn on restart mode, in which VLB assumes that the Pose

fed to it during apply() has already been modified by the manager. (default False)

In restart mode, VLB only runs the manager’s dummy modify

capability during apply() to get the mapping info.

C++: protocols::forge::components::VarLengthBuild::restart_mode() const –> bool

  1. restart_mode(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

Flag to turn on restart mode, in which VLB assumes that the Pose

fed to it during apply() has already been modified by the manager. (default False)

In restart mode, VLB only runs the manager’s dummy modify

capability during apply() to get the mapping info.

C++: protocols::forge::components::VarLengthBuild::restart_mode(const bool) –> void

scorefunction(*args, **kwargs)

Overloaded function.

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set ScoreFunction used during build

C++: protocols::forge::components::VarLengthBuild::scorefunction(const class core::scoring::ScoreFunction &) –> void

  1. scorefunction(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, sfx: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

set ScoreFunction used during build

C++: protocols::forge::components::VarLengthBuild::scorefunction(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_abego(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, abego: pyrosetta.rosetta.utility.vector1_std_string) None

set abego definition for fragments

C++: protocols::forge::components::VarLengthBuild::set_abego(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> 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 &

use_fullmer(*args, **kwargs)

Overloaded function.

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> bool

also use fragments spanning the entire length of a loop?

(default false)

C++: protocols::forge::components::VarLengthBuild::use_fullmer() const –> bool

  1. use_fullmer(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, flag: bool) -> None

also use fragments spanning the entire length of a loop?

C++: protocols::forge::components::VarLengthBuild::use_fullmer(const bool) –> void

vall_memory_usage(*args, **kwargs)

Overloaded function.

  1. vall_memory_usage(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild) -> pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum

option dictating whether to keep VallLibrary in memory or clear

it under certain circumstances after picking fragments. (default KEEP_IN_MEMORY)

C++: protocols::forge::components::VarLengthBuild::vall_memory_usage() const –> enum protocols::forge::components::VLB_VallMemoryUsage::Enum

  1. vall_memory_usage(self: pyrosetta.rosetta.protocols.forge.components.VarLengthBuild, level: pyrosetta.rosetta.protocols.forge.components.VLB_VallMemoryUsage.Enum) -> None

option dictating whether to keep VallLibrary in memory or clear

it under certain circumstances after picking fragments.

C++: protocols::forge::components::VarLengthBuild::vall_memory_usage(const enum protocols::forge::components::VLB_VallMemoryUsage::Enum) –> void