nonlocal

Bindings for protocols::nonlocal namespace

class pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

User-specified, per-residue sampling probabilities allow fine grained control over the simulation.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover, policy: pyrosetta.rosetta.protocols.nonlocal.Policy, probs: pyrosetta.rosetta.utility.vector1_double) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover, arg0: pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Inserts a single fragment into pose.

Insertion position is chosen in a biased manner using the per-residue probabilities provided in the constructor. The decision on which fragment to insert from the fragment library is delegated to the policy specified in the constructor.

Respects the underlying kinematics of the system.

C++: protocols::nonlocal::BiasedFragmentMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover, : pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover) → pyrosetta.rosetta.protocols.nonlocal.BiasedFragmentMover

C++: protocols::nonlocal::BiasedFragmentMover::operator=(const class protocols::nonlocal::BiasedFragmentMover &) –> class protocols::nonlocal::BiasedFragmentMover &

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>

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

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

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

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

fpd

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

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

get_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.nonlocal.BiasedFragmentMover) → str

Returns the name of this mover

C++: protocols::nonlocal::BiasedFragmentMover::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

name() → str

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

register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.nonlocal.Chunk

Bases: pybind11_builtins.pybind11_object

region of sequence and knowledge of how to sample insertion positions from it according to an underlying distribution. Certain residues within the region may not be movable. Current behavior mimics but improves upon existing end-biased selection.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.Chunk, region: pyrosetta.rosetta.protocols.nonlocal.Region, movable: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.Chunk, arg0: pyrosetta.rosetta.protocols.nonlocal.Chunk) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.nonlocal.Chunk, other: pyrosetta.rosetta.protocols.nonlocal.Chunk) → pyrosetta.rosetta.protocols.nonlocal.Chunk

Assignment operator

C++: protocols::nonlocal::Chunk::operator=(const class protocols::nonlocal::Chunk &) –> class protocols::nonlocal::Chunk &

choose(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → int

Chooses an allowable insertion position on [start, stop] according

to the probability distribution

C++: protocols::nonlocal::Chunk::choose() const –> unsigned long

is_movable(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → bool

Returns true if at least one position on [start(), stop()] is movable

C++: protocols::nonlocal::Chunk::is_movable() const –> bool

length(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → int

Returns the length of this region

C++: protocols::nonlocal::Chunk::length() const –> unsigned long

start(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → int

Lower boundary of this chunk

C++: protocols::nonlocal::Chunk::start() const –> unsigned long

stop(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → int

Upper boundary of this chunk

C++: protocols::nonlocal::Chunk::stop() const –> unsigned long

valid(self: pyrosetta.rosetta.protocols.nonlocal.Chunk) → bool

Returns true if there is at least one valid insertion position in

the closed region [start(), stop()], false otherwise.

C++: protocols::nonlocal::Chunk::valid() const –> bool

class pyrosetta.rosetta.protocols.nonlocal.HelixRotate

Bases: pyrosetta.rosetta.protocols.moves.Mover

axis defined by its first and last residues. Makes no assumptions about the kinematics of the system.

TODO(cmiles) Improved handling of kinked helices

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, helix: pyrosetta.rosetta.protocols.loops.Loop, degrees: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, arg0: pyrosetta.rosetta.protocols.nonlocal.HelixRotate) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, pose: pyrosetta.rosetta.core.pose.Pose) → None

Rotates the helix by the specified number of degrees

C++: protocols::nonlocal::HelixRotate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, : pyrosetta.rosetta.protocols.nonlocal.HelixRotate) → pyrosetta.rosetta.protocols.nonlocal.HelixRotate

C++: protocols::nonlocal::HelixRotate::operator=(const class protocols::nonlocal::HelixRotate &) –> class protocols::nonlocal::HelixRotate &

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.nonlocal.HelixRotate) → pyrosetta.rosetta.protocols.moves.Mover

Creates a new instance with the copy constructor

C++: protocols::nonlocal::HelixRotate::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.nonlocal.HelixRotate) → pyrosetta.rosetta.protocols.moves.Mover

Creates a new instance with the default constructor

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

get_degrees(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate) → float

Returns the number of degrees to rotate the helix

C++: protocols::nonlocal::HelixRotate::get_degrees() const –> double

get_helix(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate) → pyrosetta.rosetta.protocols.loops.Loop

Returns the helix to be modified

C++: protocols::nonlocal::HelixRotate::get_helix() const –> const class protocols::loops::Loop &

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.nonlocal.HelixRotate) → str

Returns the protocol’s name

C++: protocols::nonlocal::HelixRotate::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

name() → str

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

register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

set_degrees(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, degrees: float) → None

Updates the number of degrees to rotate the helix

C++: protocols::nonlocal::HelixRotate::set_degrees(double) –> void

set_helix(self: pyrosetta.rosetta.protocols.nonlocal.HelixRotate, helix: pyrosetta.rosetta.protocols.loops.Loop) → None

Updates the helix to be modified

C++: protocols::nonlocal::HelixRotate::set_helix(const class protocols::loops::Loop &) –> void

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

setter for poses contained for rms

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

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

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

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

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.nonlocal.Policy

Bases: pybind11_builtins.pybind11_object

fragment from set of possibilities. This class is based on the observation that fragment insertion methods differ primarily in the manner in which they choose from among a set of possibilities.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.Policy, fragments: pyrosetta.rosetta.core.fragment.FragSet) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.Policy, arg0: pyrosetta.rosetta.protocols.nonlocal.Policy) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.nonlocal.Policy, : pyrosetta.rosetta.protocols.nonlocal.Policy) → pyrosetta.rosetta.protocols.nonlocal.Policy

C++: protocols::nonlocal::Policy::operator=(const class protocols::nonlocal::Policy &) –> class protocols::nonlocal::Policy &

choose(self: pyrosetta.rosetta.protocols.nonlocal.Policy, frame: pyrosetta.rosetta.core.fragment.Frame, pose: pyrosetta.rosetta.core.pose.Pose) → int

Selects a single fragment from a set of possibilities given the

current status of the pose.

C++: protocols::nonlocal::Policy::choose(const class core::fragment::Frame &, const class core::pose::Pose &) –> unsigned long

fragments(self: pyrosetta.rosetta.protocols.nonlocal.Policy) → pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::nonlocal::Policy::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

class pyrosetta.rosetta.protocols.nonlocal.SheetTranslate

Bases: pyrosetta.rosetta.protocols.moves.Mover

the axis defined by its first and last residues. Makes no assumptions about the kinematics of the system.

TODO(cmiles) Consider having the user define the axis of translation. TODO(cmiles) Improved handling of curved sheets

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, sheet: pyrosetta.rosetta.protocols.loops.Loop, distance_ang: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, arg0: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

apply(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, pose: pyrosetta.rosetta.core.pose.Pose) → None

Translates the sheet by the specified distance (in Angstroms)

C++: protocols::nonlocal::SheetTranslate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, : pyrosetta.rosetta.protocols.nonlocal.SheetTranslate) → pyrosetta.rosetta.protocols.nonlocal.SheetTranslate

C++: protocols::nonlocal::SheetTranslate::operator=(const class protocols::nonlocal::SheetTranslate &) –> class protocols::nonlocal::SheetTranslate &

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.nonlocal.SheetTranslate) → pyrosetta.rosetta.protocols.moves.Mover

Creates a new instance with the copy constructor

C++: protocols::nonlocal::SheetTranslate::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.nonlocal.SheetTranslate) → pyrosetta.rosetta.protocols.moves.Mover

Creates a new instance with the default constructor

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

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

fpd

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

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

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

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

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

A tag is a unique identifier used to identify structures produced

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

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

get_distance(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate) → float

Returns the distance (in Angstroms) to translate the sheet

C++: protocols::nonlocal::SheetTranslate::get_distance() const –> double

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.nonlocal.SheetTranslate) → str

Returns the protocol’s name

C++: protocols::nonlocal::SheetTranslate::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_sheet(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate) → pyrosetta.rosetta.protocols.loops.Loop

Returns the sheet to be modified

C++: protocols::nonlocal::SheetTranslate::get_sheet() const –> const class protocols::loops::Loop &

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

name() → str

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

register_options() → None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

set_distance(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, distance_ang: float) → None

Updates the distance (in Angstroms) to translate the sheet

C++: protocols::nonlocal::SheetTranslate::set_distance(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_sheet(self: pyrosetta.rosetta.protocols.nonlocal.SheetTranslate, sheet: pyrosetta.rosetta.protocols.loops.Loop) → None

Updates the sheet to be modified

C++: protocols::nonlocal::SheetTranslate::set_sheet(const class protocols::loops::Loop &) –> void

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

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

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy

Bases: pyrosetta.rosetta.protocols.nonlocal.Policy

that, when applied to the pose, minimizes total distortion (“smooth move”).

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy, fragments: pyrosetta.rosetta.core.fragment.FragSet) -> None
2. __init__(self: pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy, arg0: pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy, : pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy) → pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy

C++: protocols::nonlocal::SmoothPolicy::operator=(const class protocols::nonlocal::SmoothPolicy &) –> class protocols::nonlocal::SmoothPolicy &

choose(self: pyrosetta.rosetta.protocols.nonlocal.SmoothPolicy, frame: pyrosetta.rosetta.core.fragment.Frame, : pyrosetta.rosetta.core.pose.Pose) → int

Given the current state of <pose>, selects the fragment in <frame>

that minimizes overall distortion

C++: protocols::nonlocal::SmoothPolicy::choose(const class core::fragment::Frame &, const class core::pose::Pose &) –> unsigned long

fragments(self: pyrosetta.rosetta.protocols.nonlocal.Policy) → pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::nonlocal::Policy::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

class pyrosetta.rosetta.protocols.nonlocal.UniformPolicy

Bases: pyrosetta.rosetta.protocols.nonlocal.Policy

possible fragments at a given position.

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.nonlocal.UniformPolicy, fragments: pyrosetta.rosetta.core.fragment.FragSet) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__le__

Return self<=value.

__lt__

Return self<value.

__ne__

Return self!=value.

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

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

assign(self: pyrosetta.rosetta.protocols.nonlocal.UniformPolicy, : pyrosetta.rosetta.protocols.nonlocal.UniformPolicy) → pyrosetta.rosetta.protocols.nonlocal.UniformPolicy

C++: protocols::nonlocal::UniformPolicy::operator=(const class protocols::nonlocal::UniformPolicy &) –> class protocols::nonlocal::UniformPolicy &

choose(self: pyrosetta.rosetta.protocols.nonlocal.UniformPolicy, frame: pyrosetta.rosetta.core.fragment.Frame, : pyrosetta.rosetta.core.pose.Pose) → int

Selects uniformly among the set of possible fragments in <frame>

C++: protocols::nonlocal::UniformPolicy::choose(const class core::fragment::Frame &, const class core::pose::Pose &) –> unsigned long

fragments(self: pyrosetta.rosetta.protocols.nonlocal.Policy) → pyrosetta.rosetta.core.fragment.FragSet

C++: protocols::nonlocal::Policy::fragments() const –> class std::shared_ptr<const class core::fragment::FragSet>

pyrosetta.rosetta.protocols.nonlocal.chunks_by_CA_CA_distance(*args, **kwargs)

Overloaded function.

1. chunks_by_CA_CA_distance(pose: pyrosetta.rosetta.core.pose.Pose, chunks: pyrosetta.rosetta.protocols.loops.Loops) -> None

Computes the distance between consecutive CA atoms. If the distance exceeds

a user-specified threshold, creates a new chunk and adds it to <chunks>. CA-CA distance threshold is retrieved from the option system (rigid::max_ca_ca_dist).

C++: protocols::nonlocal::chunks_by_CA_CA_distance(const class core::pose::Pose &, class std::shared_ptr<class protocols::loops::Loops>) –> void

2. chunks_by_CA_CA_distance(pose: pyrosetta.rosetta.core.pose.Pose, chunks: pyrosetta.rosetta.protocols.loops.Loops, threshold: float) -> None

Computes the distance between consecutive CA atoms. If the distance exceeds

<threshold>, creates a new chunk and adds it to <chunks>.

C++: protocols::nonlocal::chunks_by_CA_CA_distance(const class core::pose::Pose &, class std::shared_ptr<class protocols::loops::Loops>, double) –> void

pyrosetta.rosetta.protocols.nonlocal.combine_and_trim(min_chunk_sz: int, num_residues: int, aligned_regions: pyrosetta.rosetta.protocols.loops.Loops, unaligned_regions: pyrosetta.rosetta.protocols.loops.Loops) → pyrosetta.rosetta.protocols.loops.Loops

Combine aligned and unaligned regions, limit size of final loop

C++: protocols::nonlocal::combine_and_trim(unsigned long, unsigned long, const class std::shared_ptr<class protocols::loops::Loops>, const class std::shared_ptr<class protocols::loops::Loops>) –> class protocols::loops::Loops

pyrosetta.rosetta.protocols.nonlocal.decompose(min_chunk_sz: int, max_chunk_sz: int, loop: pyrosetta.rosetta.protocols.loops.Loop, pieces: pyrosetta.rosetta.utility.vector1_protocols_loops_Loop) → None

Recursively decomposes <loop> into a series of <pieces>, each having

length less than or equal to <max_length>.

C++: protocols::nonlocal::decompose(unsigned long, unsigned long, const class protocols::loops::Loop &, class utility::vector1<class protocols::loops::Loop, class std::allocator<class protocols::loops::Loop> > *) –> void

pyrosetta.rosetta.protocols.nonlocal.emit_intermediate(pose: pyrosetta.rosetta.core.pose.Pose, file: str) → None

If -abinitio:debug is enabled, writes <pose> to <file>.

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

pyrosetta.rosetta.protocols.nonlocal.find_regions_with_minimum_size(alignment: pyrosetta.rosetta.core.sequence.SequenceAlignment, unaligned_region_min_sz: int, aligned_regions: pyrosetta.rosetta.protocols.loops.Loops, unaligned_regions: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::nonlocal::find_regions_with_minimum_size(const class core::sequence::SequenceAlignment &, const unsigned long, class std::shared_ptr<class protocols::loops::Loops> &, class std::shared_ptr<class protocols::loops::Loops> &) –> void

pyrosetta.rosetta.protocols.nonlocal.get_per_residue_score(rsd_idx: int, scoretype: pyrosetta.rosetta.core.scoring.ScoreType, pose: pyrosetta.rosetta.core.pose.Pose) → float

Returns the unweighted score of the ScoreType for the given residue. Assumes that the Pose has recently been scored by ScoreFunction with non-zero weight for the ScoreType.

C++: protocols::nonlocal::get_per_residue_score(unsigned long, enum core::scoring::ScoreType, const class core::pose::Pose &) –> double

pyrosetta.rosetta.protocols.nonlocal.limit_chunk_size(min_chunk_sz: int, max_chunk_sz: int, regions: pyrosetta.rosetta.protocols.loops.Loops) → None

Best-effort attempt to limit the length of a chunk by recursively

decomposing <regions> such that min_chunk_sz <= |chunk| <= max_chunk_sz.

C++: protocols::nonlocal::limit_chunk_size(unsigned long, unsigned long, class std::shared_ptr<class protocols::loops::Loops> &) –> void