checker

Bindings for protocols::stepwise::modeler::rna::checker namespace

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker

Bases: pybind11_object

base_atr_score(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_atr_score() const –> double

base_rep_score(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::base_rep_score() const –> double

check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, current_pose_screen: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::check_screen(class core::pose::Pose &) –> bool

count_data(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) → pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::count_data() const –> const class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &

delta_atr_score(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_atr_score() const –> double

delta_rep_score(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::delta_rep_score() const –> double

set_extra_loose_rep_cutoff(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::set_extra_loose_rep_cutoff(const bool &) –> void

set_loose_rep_cutoff(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_AtrRepChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_AtrRepChecker::set_loose_rep_cutoff(const bool &) –> void

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker

Bases: pybind11_object

allow_base_pair_only_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::allow_base_pair_only_screen() const –> const bool &

check_centroid_interaction(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, moving_res_base_stub: pyrosetta.rosetta.core.kinematics.Stub, count_data: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_centroid_interaction(const class core::kinematics::Stub &, class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &) –> bool

check_that_terminal_res_are_unstacked(*args, **kwargs)

Overloaded function.

  1. check_that_terminal_res_are_unstacked(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) -> bool

  2. check_that_terminal_res_are_unstacked(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, verbose: bool) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::check_that_terminal_res_are_unstacked(const bool) –> bool

found_centroid_interaction(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::found_centroid_interaction() const –> bool

set_allow_base_pair_only_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_allow_base_pair_only_screen(const bool) –> void

set_floating_base(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::set_floating_base(const bool) –> void

update_base_stub_list_and_check_centroid_interaction(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose: pyrosetta.rosetta.core.pose.Pose, count_data: pyrosetta.rosetta.protocols.stepwise.modeler.rna.StepWiseRNA_CountStruct) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list_and_check_centroid_interaction(const class core::pose::Pose &, class protocols::stepwise::modeler::rna::StepWiseRNA_CountStruct &) –> bool

update_base_stub_list_and_check_that_terminal_res_are_unstacked(*args, **kwargs)

Overloaded function.

  1. update_base_stub_list_and_check_that_terminal_res_are_unstacked(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

  2. update_base_stub_list_and_check_that_terminal_res_are_unstacked(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_BaseCentroidChecker, pose: pyrosetta.rosetta.core.pose.Pose, reinitialize: bool) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_BaseCentroidChecker::update_base_stub_list_and_check_that_terminal_res_are_unstacked(const class core::pose::Pose &, const bool) –> bool

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker

Bases: pybind11_object

check_chain_closable_geometry(*args, **kwargs)

Overloaded function.

  1. check_chain_closable_geometry(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, xyz_1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_2: pyrosetta.rosetta.numeric.xyzVector_double_t) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &) const –> bool

  1. check_chain_closable_geometry(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, five_prime_residue: pyrosetta.rosetta.core.conformation.Residue, three_prime_residue: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry(const class core::conformation::Residue &, const class core::conformation::Residue &) const –> bool

check_screen(*args, **kwargs)

Overloaded function.

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

  2. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose: pyrosetta.rosetta.core.pose.Pose, strict: bool) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen(const class core::pose::Pose &, const bool) const –> bool

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, moving_pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, is_prepend: bool) -> bool

  2. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, moving_pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, is_prepend: bool, strict: bool) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen(const class core::pose::Pose &, const class core::pose::Pose &, const bool, const bool) const –> bool

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose: pyrosetta.rosetta.core.pose.Pose, rsd_at_origin_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, moving_res_base_stub: pyrosetta.rosetta.core.kinematics.Stub, reference_res: int) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::kinematics::Stub &, const unsigned long &) const –> bool

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker, pose_data_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, rsd_at_origin_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, moving_res_base_stub: pyrosetta.rosetta.core.kinematics.Stub, reference_res: int) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_screen(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::kinematics::Stub &, const unsigned long &) const –> bool

dist_squared(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::dist_squared() const –> const double &

five_prime_chain_break_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) → int

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::five_prime_chain_break_res() const –> const unsigned long &

max_dist_squared(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) → float

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::max_dist_squared() const –> const double &

three_prime_chain_break_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosableGeometryChecker) → int

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::three_prime_chain_break_res() const –> const unsigned long &

class pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::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 &

chain_break_screening_general(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, chain_break_screening_pose: pyrosetta.rosetta.core.pose.Pose, chainbreak_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, five_: int) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::chain_break_screening_general(class core::pose::Pose &, const class std::shared_ptr<class core::scoring::ScoreFunction> &, const unsigned long) –> bool

check_loop_closed(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_loop_closed(const class core::pose::Pose &) –> bool

check_screen(*args, **kwargs)

Overloaded function.

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_screen() –> bool

  1. check_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::check_screen(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.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>

copy_CCD_torsions(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::copy_CCD_torsions(class core::pose::Pose &) const –> void

copy_CCD_torsions_general(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, pose: pyrosetta.rosetta.core.pose.Pose, five_prime_res: int, three_prime_res: int) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::copy_CCD_torsions_general(class core::pose::Pose &, const unsigned long, const unsigned long) const –> 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>

five_prime_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) → int

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::five_prime_res() const –> const unsigned long &

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_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.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) → str

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.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

pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::pose() –> class core::pose::Pose &

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

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_reinitialize_CCD_torsions(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_ChainClosureChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_ChainClosureChecker::set_reinitialize_CCD_torsions(const bool &) –> 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.stepwise.modeler.rna.checker.RNA_VDW_BinChecker

Bases: pybind11_object

FARFAR_setup_using_user_input_VDW_pose(*args, **kwargs)

Overloaded function.

  1. FARFAR_setup_using_user_input_VDW_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, VDW_rep_screen_pose_info: pyrosetta.rosetta.utility.vector1_std_string, const_working_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &) –> void

  1. FARFAR_setup_using_user_input_VDW_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, All_VDW_rep_screen_pose_info: pyrosetta.rosetta.utility.vector1_std_string, const_working_pose: pyrosetta.rosetta.core.pose.Pose, include_side_chains: bool) -> None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::FARFAR_setup_using_user_input_VDW_pose(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &, const bool) –> void

VDW_rep_screen(*args, **kwargs)

Overloaded function.

  1. VDW_rep_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int, rsd_at_origin: pyrosetta.rosetta.core.conformation.Residue, moving_res_base_stub: pyrosetta.rosetta.core.kinematics.Stub) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(const class core::pose::Pose &, const unsigned long &, const class core::conformation::Residue &, const class core::kinematics::Stub &) –> bool

  1. VDW_rep_screen(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose: pyrosetta.rosetta.core.pose.Pose, moving_res: int) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen(const class core::pose::Pose &, const unsigned long &) –> bool

VDW_rep_screen_with_act_pose(*args, **kwargs)

Overloaded function.

  1. VDW_rep_screen_with_act_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose: pyrosetta.rosetta.core.pose.Pose, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> bool

  2. VDW_rep_screen_with_act_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, screening_pose: pyrosetta.rosetta.core.pose.Pose, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, local_verbose: bool) -> bool

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen_with_act_pose(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> bool

align_working_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, working_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::align_working_pose(class core::pose::Pose &) const –> void

create_VDW_screen_bin(*args, **kwargs)

Overloaded function.

  1. create_VDW_screen_bin(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose: pyrosetta.rosetta.core.pose.Pose, ignore_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, is_prepend: bool, reference_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

  2. create_VDW_screen_bin(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose: pyrosetta.rosetta.core.pose.Pose, ignore_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, is_prepend: bool, reference_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, verbose: bool) -> None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const class numeric::xyzVector<double> &, const bool) –> void

  1. create_VDW_screen_bin(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, VDW_rep_screen_info_list: pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo, reference_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, verbose: bool) -> None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(const class utility::vector1<class core::pose::rna::VDW_RepScreenInfo, class std::allocator<class core::pose::rna::VDW_RepScreenInfo> > &, const class numeric::xyzVector<double> &, const bool) –> void

  1. create_VDW_screen_bin(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose_list: pyrosetta.rosetta.utility.vector1_core_pose_Pose, list_of_ignore_res_list: pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t, list_of_is_prepend: pyrosetta.rosetta.utility.vector1_bool, reference_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t, verbose: bool) -> None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::create_VDW_screen_bin(const class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, const class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > &, const class utility::vector1<bool, class std::allocator<bool> >, const class numeric::xyzVector<double> &, const bool) –> void

get_VDW_align_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::get_VDW_align_res() –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

reference_xyz_consistency_check(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, inputted_reference_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::reference_xyz_consistency_check(const class numeric::xyzVector<double> &) const –> void

set_VDW_rep_alignment_RMSD_CUTOFF(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting: float) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_alignment_RMSD_CUTOFF(const double &) –> void

set_VDW_rep_delete_matching_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_VDW_rep_delete_matching_res(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_num_clash_atom_cutoff(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting: int) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_num_clash_atom_cutoff(const unsigned long) –> void

set_output_pdb(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting: bool) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_output_pdb(const bool) –> void

set_physical_pose_clash_dist_cutoff(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, setting: float) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::set_physical_pose_clash_dist_cutoff(const double &) –> void

setup_using_user_input_VDW_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, All_VDW_rep_screen_pose_info: pyrosetta.rosetta.utility.vector1_std_string, const_working_pose: pyrosetta.rosetta.core.pose.Pose, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_user_input_VDW_pose(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class core::pose::Pose &, const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> void

setup_using_working_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, const_working_pose: pyrosetta.rosetta.core.pose.Pose, working_parameters: protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_using_working_pose(const class core::pose::Pose &, const class std::shared_ptr<const class protocols::stepwise::modeler::working_parameters::StepWiseWorkingParameters> &) –> void

setup_working_alignment(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, working_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::setup_working_alignment(class core::pose::Pose &) –> void

update_VDW_screen_bin(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker, pose: pyrosetta.rosetta.core.pose.Pose, ignore_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, is_prepend: bool, outfile_act: pyrosetta.rosetta.std.ofstream) → None

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::update_VDW_screen_bin(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, class std::basic_ofstream<char> &) –> void

user_inputted_VDW_screen_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.rna.checker.RNA_VDW_BinChecker) → bool

C++: protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::user_inputted_VDW_screen_pose() const –> bool