ub_e2c

Bindings for protocols::ub_e2c namespace

class pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler

Bases: Mover

CSP_fraction(*args, **kwargs)

Overloaded function.

1. CSP_fraction(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) -> float

2. CSP_fraction(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, non_CSP: bool) -> float

3. CSP_fraction(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, non_CSP: bool, trim: bool) -> float

4. CSP_fraction(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, non_CSP: bool, trim: bool, swap: bool) -> float

C++: protocols::ub_e2c::ubi_e2c_modeler::CSP_fraction(const class core::pose::Pose &, bool, bool, bool) –> double

apply(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::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 &

calc_Lrmsd(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, ubiquitin: int) → float

C++: protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long) –> double

calc_interaction_energy(*args, **kwargs)

Overloaded function.

1. calc_interaction_energy(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) -> float

2. calc_interaction_energy(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, dimer: bool) -> float

C++: protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy(const class core::pose::Pose &, bool) –> double

centroid_filter(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ub_e2c::ubi_e2c_modeler::centroid_filter(class core::pose::Pose &) –> bool

centroid_mode_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation(class core::pose::Pose &) –> double

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.ub_e2c.ubi_e2c_modeler) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ub_e2c::ubi_e2c_modeler::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_native(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(class core::pose::Pose &) –> void

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

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

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

fullatom_filter(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter(class core::pose::Pose &) –> bool

fullatom_mode_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation(class core::pose::Pose &) –> double

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.ub_e2c.ubi_e2c_modeler) → str

C++: protocols::ub_e2c::ubi_e2c_modeler::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 > > &

init_d77_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation(class core::pose::Pose &) –> void

init_k48r_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(class core::pose::Pose &) –> void

initial_cter_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation(class core::pose::Pose &) –> void

initial_perturbation(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation(class core::pose::Pose &) –> double

initial_repack(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::initial_repack(class core::pose::Pose &) –> void

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

optimize_cov_bond(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond(class core::pose::Pose &) –> 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

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

restore_cter(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, without_cter: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::restore_cter(class core::pose::Pose &, class core::pose::Pose) –> void

restrict_to_interfacial_loop_packing(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing(class core::pose::Pose &) –> 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_default(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::set_default() –> void

set_e2g2_diubi_fold_tree(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(class core::pose::Pose &) –> 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

setup_complex_fold_tree(*args, **kwargs)

Overloaded function.

1. setup_complex_fold_tree(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) -> None

2. setup_complex_fold_tree(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, trim: bool) -> None

C++: protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree(class core::pose::Pose &, bool) –> void

setup_key_residues(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(const class core::pose::Pose &) –> void

setup_move_maps(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps() –> void

setup_packer_task(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task(class core::pose::Pose &) –> void

setup_simple_fold_tree(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, jumppoint1: int, cutpoint: int, jumppoint2: int, nres: int, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree(unsigned long, unsigned long, unsigned long, unsigned long, class core::pose::Pose &) –> 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

trim_cter(self: pyrosetta.rosetta.protocols.ub_e2c.ubi_e2c_modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ub_e2c::ubi_e2c_modeler::trim_cter(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

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

Get the set ‘type’ string

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