simple_moves

• a3b_hbs
• asym_fold_and_dock
• bb_sampler
• bin_transitions
• chiral
• hbs
• oop
• rational_mc
• sidechain_moves
• symmetry
• triazolamer

Bindings for protocols::simple_moves namespace

class pyrosetta.rosetta.protocols.simple_moves.AcceptedScores

Bases: pyrosetta.rosetta.utility.vector1_double

Represents a set of filter scores that have been accepted

__bool__(self: pyrosetta.rosetta.utility.vector1_double) → bool

Check whether the list is nonempty

__contains__(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → bool

return true if item in the container

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(self: pyrosetta.rosetta.utility.vector1_double, arg0: pyrosetta.rosetta.utility.vector1_double) → bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getitem__(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → float

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores, iteration: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores, iteration: int, rank_score: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores, iteration: int, rank_score: float, scores: pyrosetta.rosetta.utility.vector1_double) -> None

__init_subclass__()

This method is called when a class is subclassed.

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

__iter__(self: pyrosetta.rosetta.utility.vector1_double) → iterator

__le__

Return self<=value.

__len__(self: pyrosetta.rosetta.utility.vector1_double) → int

__lt__

Return self<value.

__ne__(self: pyrosetta.rosetta.utility.vector1_double, arg0: pyrosetta.rosetta.utility.vector1_double) → bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.utility.vector1_double) → str

__setattr__

Implement setattr(self, name, value).

__setitem__(self: pyrosetta.rosetta.utility.vector1_double, arg0: int, arg1: float) → None

__sizeof__() → int

size of object in memory, in bytes

__str__(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores) → str

__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).

append(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → None

adds an element to the end

assign(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores, : pyrosetta.rosetta.protocols.simple_moves.AcceptedScores) → pyrosetta.rosetta.protocols.simple_moves.AcceptedScores

C++: protocols::simple_moves::AcceptedScores::operator=(const class protocols::simple_moves::AcceptedScores &) –> class protocols::simple_moves::AcceptedScores &

back(self: pyrosetta.rosetta.utility.vector1_double) → float

access the last element

capacity(self: pyrosetta.rosetta.utility.vector1_double) → int

returns the number of elements that can be held in currently allocated storage

clear(self: pyrosetta.rosetta.utility.vector1_double) → None

clears the contents

count(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → int

counts the elements that are equal to value

erase(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None

erases element at index

front(self: pyrosetta.rosetta.utility.vector1_double) → float

access the first element

iteration(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores) → int

C++: protocols::simple_moves::AcceptedScores::iteration() const –> unsigned long

l(self: pyrosetta.rosetta.utility.vector1_double) → int

lower index

max_size(self: pyrosetta.rosetta.utility.vector1_double) → int

returns the maximum possible number of elements

pop(*args, **kwargs)

Overloaded function.

1. pop(self: pyrosetta.rosetta.utility.vector1_double) -> float

remove and return last item

2. pop(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) -> float

remove and return item at index

rank_score(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores) → float

C++: protocols::simple_moves::AcceptedScores::rank_score() const –> double

remove(self: pyrosetta.rosetta.utility.vector1_double, arg0: float) → None

Remove the first item from the list whose value is x. It is an error if there is no such item.

reserve(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None

reserves storage

resize(self: pyrosetta.rosetta.utility.vector1_double, arg0: int) → None

changes the number of elements stored

set_rank_score(self: pyrosetta.rosetta.protocols.simple_moves.AcceptedScores, rank_score: float) → None

C++: protocols::simple_moves::AcceptedScores::set_rank_score(const double) –> void

shrink_to_fit(self: pyrosetta.rosetta.utility.vector1_double) → None

reduces memory usage by freeing unused memory

u(self: pyrosetta.rosetta.utility.vector1_double) → int

upper index

class pyrosetta.rosetta.protocols.simple_moves.AddJobPairData

Bases: pyrosetta.rosetta.protocols.moves.Mover

Add an arbitrary piece of data to the current Job, which will be output in the silent file, database, etc. This is useful for adding metadata to keep track of data generated using multiple experimental conditions. Currently ONLY RosettaScript interface supported.

The data appended to the Job consists of a key and a value. The key is a string, and the value can be either a real or string.

__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.simple_moves.AddJobPairData) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, arg0: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) -> 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.simple_moves.AddJobPairData, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::AddJobPairData::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AddJobPairData, : pyrosetta.rosetta.protocols.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.simple_moves.AddJobPairData

C++: protocols::simple_moves::AddJobPairData::operator=(const class protocols::simple_moves::AddJobPairData &) –> class protocols::simple_moves::AddJobPairData &

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.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::AddJobPairData::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.simple_moves.AddJobPairData) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::AddJobPairData::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.simple_moves.AddJobPairData) → str

C++: protocols::simple_moves::AddJobPairData::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

mover_name() → str

C++: protocols::simple_moves::AddJobPairData::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::AddJobPairData::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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.simple_moves.AlignChainMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Align a chain in the working pose to a chain. CA superposition

source_chain: the chain number in the working pose. 0 means the entire pose. target_chain: the chain number in the target pose. 0 means the entire pose. **target and source chains must have the same length of residues.

__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.simple_moves.AlignChainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> 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.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::AlignChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, : pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.simple_moves.AlignChainMover

C++: protocols::simple_moves::AlignChainMover::operator=(const class protocols::simple_moves::AlignChainMover &) –> class protocols::simple_moves::AlignChainMover &

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.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::AlignChainMover::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.simple_moves.AlignChainMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::AlignChainMover::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.simple_moves.AlignChainMover) → str

C++: protocols::simple_moves::AlignChainMover::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

mover_name() → str

C++: protocols::simple_moves::AlignChainMover::mover_name() –> std::string

name() → str

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

pose(*args, **kwargs)

Overloaded function.

1. pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::simple_moves::AlignChainMover::pose() const –> class std::shared_ptr<class core::pose::Pose>

2. pose(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::AlignChainMover::pose(class std::shared_ptr<class core::pose::Pose>) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::AlignChainMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

source_chain(*args, **kwargs)

Overloaded function.

1. source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int

C++: protocols::simple_moves::AlignChainMover::source_chain() const –> unsigned long

2. source_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None

C++: protocols::simple_moves::AlignChainMover::source_chain(const unsigned long) –> void

target_chain(*args, **kwargs)

Overloaded function.

1. target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover) -> int

C++: protocols::simple_moves::AlignChainMover::target_chain() const –> unsigned long

2. target_chain(self: pyrosetta.rosetta.protocols.simple_moves.AlignChainMover, s: int) -> None

C++: protocols::simple_moves::AlignChainMover::target_chain(const unsigned long) –> 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.simple_moves.BBDihedralSamplerMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover interface to BBDihedralSampler ( 1D ). Samples using BBDihedralSamplers randomly using residues set in the movemap. If multiple samplers are given, will randomly sample on them.

__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.simple_moves.BBDihedralSamplerMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, arg0: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → str

__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).

add_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) → None

Add a sampler to this mover.

C++: protocols::simple_moves::BBDihedralSamplerMover::add_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BBDihedralSamplerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, : pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover

C++: protocols::simple_moves::BBDihedralSamplerMover::operator=(const class protocols::simple_moves::BBDihedralSamplerMover &) –> class protocols::simple_moves::BBDihedralSamplerMover &

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.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBDihedralSamplerMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBDihedralSamplerMover) → str

C++: protocols::simple_moves::BBDihedralSamplerMover::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_dihedral_mask(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, mask: pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t) → None

Limit the torsions that are sampled using a mask.

Mask is a vector of torsions we are allowed to sample at each residue.

NOT every residue must be present - only the ones we need to mask. This helps for carbohydrates, since not every residue has all possible dihedrals, even if we have samplers to use.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_dihedral_mask(class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > >) –> 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_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Sets residues from a residue selector.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_sampler(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, sampler: pyrosetta.rosetta.protocols.simple_moves.bb_sampler.BBDihedralSampler) → None

Set a single sampler this mover will use.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_sampler(class std::shared_ptr<class protocols::simple_moves::bb_sampler::BBDihedralSampler>) –> void

set_single_resnum(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, resnum: int) → None

Set a single resnum instead of a movemap.

C++: protocols::simple_moves::BBDihedralSamplerMover::set_single_resnum(unsigned long) –> 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.simple_moves.BBDihedralSamplerMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.BBDihedralSamplerMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::BBDihedralSamplerMover::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.simple_moves.BBG8T3AMover

Bases: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

a particular gaussian mover from the original paper

using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end

__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.simple_moves.BBG8T3AMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover, arg0: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) -> 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.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover, : pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover) → pyrosetta.rosetta.protocols.simple_moves.BBG8T3AMover

C++: protocols::simple_moves::BBG8T3AMover::operator=(const class protocols::simple_moves::BBG8T3AMover &) –> class protocols::simple_moves::BBG8T3AMover &

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.simple_moves.BBG8T3AMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::BBG8T3AMover::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>

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) → None

C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) → None

C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> 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>

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → float

calculate L matrix and update pose

C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double

get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float

calculate L’, update last_proposal_density

C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

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

fpd

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

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.simple_moves.BBG8T3AMover) → str

C++: protocols::simple_moves::BBG8T3AMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::init() –> void

init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Generates the movemap used by this mover for the given pose

C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.

C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string

name() → str

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → bool

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::BBGaussianMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) → None

C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> 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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

dummy

C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

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

update_counting_last_PDR(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : float) → None

C++: protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

Bases: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

the basic class for implementing Gaussian Perturbation of bb

“Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space” “The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158.” Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: “pivot” update the bb conformation, or followed by a chainclosure method (BBConRot)

__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.simple_moves.BBGaussianMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, arg0: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) -> 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.simple_moves.BBGaussianMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BBGaussianMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover

C++: protocols::simple_moves::BBGaussianMover::operator=(const class protocols::simple_moves::BBGaussianMover &) –> class protocols::simple_moves::BBGaussianMover &

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.simple_moves.BBGaussianMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::BBGaussianMover::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>

factorA(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fA: float) → None

C++: protocols::simple_moves::BBGaussianMover::factorA(const double) –> void

factorB(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, fB: float) → None

C++: protocols::simple_moves::BBGaussianMover::factorB(const double) –> void

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> 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>

get_A(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::get_A() –> void

get_G(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::get_G() –> void

get_L_move(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → float

calculate L matrix and update pose

C++: protocols::simple_moves::BBGaussianMover::get_L_move(class core::pose::Pose &) –> double

get_L_prime(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float

calculate L’, update last_proposal_density

C++: protocols::simple_moves::BBGaussianMover::get_L_prime() –> double

get_VdRdPhi(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BBGaussianMover::get_VdRdPhi(const class core::pose::Pose &) –> void

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

fpd

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

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.simple_moves.BBGaussianMover) → str

C++: protocols::simple_moves::BBGaussianMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → None

C++: protocols::simple_moves::BBGaussianMover::init() –> void

init_kic_loop(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, looplength: int, mm: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::simple_moves::BBGaussianMover::init_kic_loop(unsigned long, class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → float

get the ratio of proposal densities for the last move

C++: protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio() –> double

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Generates the movemap used by this mover for the given pose

C++: protocols::simple_moves::BBGaussianMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BBGaussianMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

The movemap_factory will be used to generate a movemap, if an explcit one hasn’t already been set.

C++: protocols::simple_moves::BBGaussianMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::BBGaussianMover::mover_name() –> std::string

name() → str

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

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover) → bool

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::BBGaussianMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

resize(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : int, : int, : int) → None

C++: protocols::simple_moves::BBGaussianMover::resize(unsigned long, unsigned long, unsigned long) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BBGaussianMover::set_preserve_detailed_balance(bool) –> 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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

dummy

C++: protocols::simple_moves::BBGaussianMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

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

update_counting_last_PDR(self: pyrosetta.rosetta.protocols.simple_moves.BBGaussianMover, : float) → None

C++: protocols::simple_moves::BBGaussianMover::update_counting_last_PDR(double) –> void

class pyrosetta.rosetta.protocols.simple_moves.BackboneMover

Bases: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover

BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.).

change this to some kind of ‘protocol’ so the MC is managed separately from conformational moves

__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__

Initialize self. See help(type(self)) for accurate signature.

__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__(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → str

__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).

angle_max(*args, **kwargs)

Overloaded function.

1. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Sets the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

2. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(‘H’, 25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

3. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures

‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None

virtual functions that get overridden or called from the inheriting classes

C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → pyrosetta.rosetta.protocols.simple_moves.BackboneMover

C++: protocols::simple_moves::BackboneMover::operator=(const class protocols::simple_moves::BackboneMover &) –> class protocols::simple_moves::BackboneMover &

backbone_mover_complex_type_namer(tag_name: str) → str

C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(class std::basic_string<char>) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None

C++: protocols::simple_moves::BackboneMover::clear() –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

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

Return a clone of the Mover object.

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

complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> 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>

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_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:

bbmover.angle_max(‘H’)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

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.simple_moves.BackboneMover) → str

C++: protocols::simple_moves::BackboneMover::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 > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::BackboneMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

name() → str

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

new_omega(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_omega() –> double

new_phi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_phi() –> double

new_psi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_psi() –> double

nmoves(*args, **kwargs)

Overloaded function.

1. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

2. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

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

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

if set, this scorefunction will be used instead of the original rama method (default = not set)

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

2. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)

Overloaded function.

1. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns the residue selector which can be used to dynamically select residues to perturb

at runtime

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : float) → None

C++: protocols::simple_moves::BackboneMover::set_angles(double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::BackboneMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)

Overloaded function.

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

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

temperature(*args, **kwargs)

Overloaded function.

1. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

Properties set/get functions

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

2. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

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

torsion_id_ranges(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

Return a list specifying which torsions may be perturbed by

apply(), and the in what range each perturbation may be.

This method should probably not be pure virtual, and in fact should probably not even exist. I searched most of the codebase, and could only find it being used in one pilot app. It is also a somewhat difficult method to write, which means that most of the implementations are either untested or no-ops. It might be better to remove the method altogether and implement it on a class-by-class basis as necessary.

C++: protocols::canonical_sampling::ThermodynamicMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

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.simple_moves.ChainSplitMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

ChainSplitMover splits a pose into two chains given a cutpoint. This may be necessary for evaluating a domain interface using classes such as the InterfaceAnalyzerMover

__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.simple_moves.ChainSplitMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, cutpoint: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) -> 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.simple_moves.ChainSplitMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ChainSplitMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover, : pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.simple_moves.ChainSplitMover

C++: protocols::simple_moves::ChainSplitMover::operator=(const class protocols::simple_moves::ChainSplitMover &) –> class protocols::simple_moves::ChainSplitMover &

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.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ChainSplitMover::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.simple_moves.ChainSplitMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ChainSplitMover::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.simple_moves.ChainSplitMover) → str

C++: protocols::simple_moves::ChainSplitMover::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.simple_moves.ChangeAndResetFoldTreeMover

Bases: pyrosetta.rosetta.protocols.moves.MoverApplyingMover

Basic mover used primarily for setting up atomic protocols, especially in generator functions.

As the Topology Broker system includes more claims and is more widely adopted, This should not be used in favor of the Broker system.

1. Holds the Pose’s original FoldTree
2. Applies its ChangeFoldTreeMover
3. Applies its Main mover
4. Returns the Pose’s original FoldTree

__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.simple_moves.ChangeAndResetFoldTreeMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover, ft_mover: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover, ft_mover: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) -> 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.simple_moves.ChangeAndResetFoldTreeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

1. Holds the Pose’s original FoldTree

2. Applies the ChangeFoldTreeMover
3. Applies the Main mover
4. Returns the Pose’s original FoldTree

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, : pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::operator=(const class protocols::simple_moves::ChangeAndResetFoldTreeMover &) –> class protocols::simple_moves::ChangeAndResetFoldTreeMover &

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.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::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.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover

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

ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover

Get the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::ft_mover() const –> class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>

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.simple_moves.ChangeAndResetFoldTreeMover) → str

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::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

mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.protocols.moves.Mover

Get the main mover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

mover_name() → str

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

Get the set ScoreFunction

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_ft_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, ft_mover: pyrosetta.rosetta.protocols.moves.ChangeFoldTreeMover) → None

Set the ChangeFoldTreeMover

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_ft_mover(class std::shared_ptr<class protocols::moves::ChangeFoldTreeMover>) –> 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_mover(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, main_mover: pyrosetta.rosetta.protocols.moves.Mover) → None

Set the main mover to apply

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ChangeAndResetFoldTreeMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the ScoreFunction.

Used ONLY for printing score information before and after the move!!

C++: protocols::simple_moves::ChangeAndResetFoldTreeMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.simple_moves.ClassicFragmentMover

Bases: pyrosetta.rosetta.protocols.simple_moves.FragmentMover

A FragmentMover that applies uniform sampling of fragments

__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.simple_moves.ClassicFragmentMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, fragset: pyrosetta.rosetta.core.fragment.FragSet) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, fragset: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, fragset: pyrosetta.rosetta.core.fragment.ConstantLengthFragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str

__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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
2. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:

mover_3mer.apply(pose)

See also:

ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover

C++: protocols::simple_moves::ClassicFragmentMover::operator=(const class protocols::simple_moves::ClassicFragmentMover &) –> class protocols::simple_moves::ClassicFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);

return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool

yields a length (window_length) of the fragment window to sample from

( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool

yields a start position (window_start) for fragment window to sample from

( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> 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.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ClassicFragmentMover::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>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)

Overloaded function.

1. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
2. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float

C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

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

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

C++: protocols::simple_moves::ClassicFragmentMover::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.simple_moves.ClassicFragmentMover) → str

C++: protocols::simple_moves::ClassicFragmentMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

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_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> 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_defaults(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

set defaults

C++: protocols::simple_moves::ClassicFragmentMover::set_defaults() –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None

C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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.simple_moves.ClassicFragmentMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ClassicFragmentMover::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

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const class std::basic_string<char> &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover will modify a given task according to a sequence profile and then call the PackRotamersMover. At every position that is designable in the task, AAs that have a probability > min_aa_probability_ and higher than the native in the sequence profile will be allowed

__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.simple_moves.ConsensusDesignMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover) -> 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.simple_moves.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ConsensusDesignMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, : pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover) → pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover

C++: protocols::simple_moves::ConsensusDesignMover::operator=(const class protocols::simple_moves::ConsensusDesignMover &) –> class protocols::simple_moves::ConsensusDesignMover &

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.simple_moves.ConsensusDesignMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

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

create_consensus_design_task(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(const class core::pose::Pose &) –> class std::shared_ptr<const class core::pack::task::PackerTask>

create_sequence_profile_constraints(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::simple_moves::ConsensusDesignMover::create_sequence_profile_constraints(const class core::pose::Pose &, const class core::pack::task::PackerTask &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

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

C++: protocols::simple_moves::ConsensusDesignMover::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.simple_moves.ConsensusDesignMover) → str

C++: protocols::simple_moves::ConsensusDesignMover::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

mover_name() → str

C++: protocols::simple_moves::ConsensusDesignMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ConsensusDesignMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_invert_task(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, setting: bool) → None

C++: protocols::simple_moves::ConsensusDesignMover::set_invert_task(bool) –> 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_sasa_cutoff(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, cutoff: float) → None

C++: protocols::simple_moves::ConsensusDesignMover::set_sasa_cutoff(double) –> 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

set_use_seqprof_constraints(self: pyrosetta.rosetta.protocols.simple_moves.ConsensusDesignMover, setting: bool) → None

C++: protocols::simple_moves::ConsensusDesignMover::set_use_seqprof_constraints(bool) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.simple_moves.ConstrainToIdealMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Idealization is generally performed by adding constraints to the Pose that keep bond lengths and angles within the appropriate ranges; then freeing those DOFs and performing minimization or sampling. This protocols::moves::Mover creates bond and angle constraints compatible with idealization; it does not modify the input Pose other than by adding constraints. If your pose is already ideal, this is likely to unidealize it. Also, it will add a LOT of degrees of freedom to your minimization, which may lead to significant slowdowns!

__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.simple_moves.ConstrainToIdealMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) -> 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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::ConstrainToIdealMover::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, pose: pyrosetta.rosetta.core.pose.Pose, mm: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::ConstrainToIdealMover::apply(class core::pose::Pose &, class core::kinematics::MoveMap &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, rhs: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover

C++: protocols::simple_moves::ConstrainToIdealMover::operator=(const class protocols::simple_moves::ConstrainToIdealMover &) –> class protocols::simple_moves::ConstrainToIdealMover &

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.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ConstrainToIdealMover::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.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ConstrainToIdealMover::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_atom_level_domain_map(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover) → pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap

getter for AtomLevelDomainMap

C++: protocols::simple_moves::ConstrainToIdealMover::get_atom_level_domain_map() const –> class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>

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.simple_moves.ConstrainToIdealMover) → str

C++: protocols::simple_moves::ConstrainToIdealMover::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_atom_level_domain_map(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) → None

setter for AtomLevelDomainMap; makes a shallow copy

C++: protocols::simple_moves::ConstrainToIdealMover::set_atom_level_domain_map(class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>) –> 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_fix_angles(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_angles(const bool &) –> void

set_fix_lengths(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_lengths(const bool &) –> void

set_fix_torsions(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_fix_torsions(const bool &) –> 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_just_polar_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_just_polar_hydrogens(const bool) –> void

set_just_rna_backbone(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: bool) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_just_rna_backbone(const bool) –> void

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

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

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

set_score_type(self: pyrosetta.rosetta.protocols.simple_moves.ConstrainToIdealMover, setting: pyrosetta.rosetta.core.scoring.ScoreType) → None

C++: protocols::simple_moves::ConstrainToIdealMover::set_score_type(const enum core::scoring::ScoreType) –> 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.simple_moves.ConvertRealToVirtualMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover for switching a residue type to all VIRTUAL.

A VIRTUAL Residue is one that is not scored or output.

If no residue_selector is set, will work on ALL residues

See also:

FAToVirtualMover

__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.simple_moves.ConvertRealToVirtualMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover) → str

__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.simple_moves.ConvertRealToVirtualMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ConvertRealToVirtualMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover, : pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover) → pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover

C++: protocols::simple_moves::ConvertRealToVirtualMover::operator=(const class protocols::simple_moves::ConvertRealToVirtualMover &) –> class protocols::simple_moves::ConvertRealToVirtualMover &

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.simple_moves.ConvertRealToVirtualMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertRealToVirtualMover::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.simple_moves.ConvertRealToVirtualMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertRealToVirtualMover::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.simple_moves.ConvertRealToVirtualMover) → str

C++: protocols::simple_moves::ConvertRealToVirtualMover::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

mover_name() → str

C++: protocols::simple_moves::ConvertRealToVirtualMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ConvertRealToVirtualMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the residue selector. If you need a particular set of residues,

use the ReturnSubsetResidueSelector.

C++: protocols::simple_moves::ConvertRealToVirtualMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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.simple_moves.ConvertRealToVirtualMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.ConvertRealToVirtualMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ConvertRealToVirtualMover::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.simple_moves.ConvertVirtualToRealMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Mover for switching from VIRTUAL residues to REAL residues.

A VIRTUAL residue is one that is not scored or output.

If no residue_selector is set, will work on ALL residues

See also:

FAToVirtualMover

__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.simple_moves.ConvertVirtualToRealMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → str

__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.simple_moves.ConvertVirtualToRealMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ConvertVirtualToRealMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, : pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover

C++: protocols::simple_moves::ConvertVirtualToRealMover::operator=(const class protocols::simple_moves::ConvertVirtualToRealMover &) –> class protocols::simple_moves::ConvertVirtualToRealMover &

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.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertVirtualToRealMover::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.simple_moves.ConvertVirtualToRealMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::ConvertVirtualToRealMover::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.simple_moves.ConvertVirtualToRealMover) → str

C++: protocols::simple_moves::ConvertVirtualToRealMover::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

mover_name() → str

C++: protocols::simple_moves::ConvertVirtualToRealMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ConvertVirtualToRealMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the residue selector. If you need a particular set of residues,

use the ReturnSubsetResidueSelector.

C++: protocols::simple_moves::ConvertVirtualToRealMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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.simple_moves.ConvertVirtualToRealMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.ConvertVirtualToRealMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::ConvertVirtualToRealMover::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.simple_moves.CopyRotamerMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to copy a rotamer (residue identity and conformation) from one position in a pose to another.

__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.simple_moves.CopyRotamerMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, arg0: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → str

__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.simple_moves.CopyRotamerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the mover

C++: protocols::simple_moves::CopyRotamerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, : pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover

C++: protocols::simple_moves::CopyRotamerMover::operator=(const class protocols::simple_moves::CopyRotamerMover &) –> class protocols::simple_moves::CopyRotamerMover &

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.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CopyRotamerMover::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.simple_moves.CopyRotamerMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CopyRotamerMover::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.simple_moves.CopyRotamerMover) → str

C++: protocols::simple_moves::CopyRotamerMover::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

mover_name() → str

C++: protocols::simple_moves::CopyRotamerMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::CopyRotamerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_copy_identity(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, setting_in: bool) → None

Set whether we’re copying the residue identity.

C++: protocols::simple_moves::CopyRotamerMover::set_copy_identity(const bool) –> void

set_copy_torsions(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, setting_in: bool) → None

Set whether we’re copying the residue side-chain torsions.

C++: protocols::simple_moves::CopyRotamerMover::set_copy_torsions(const bool) –> 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_target_res_index(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, index_in: int) → None

Set pose index of the residue TO which we’re copying.

C++: protocols::simple_moves::CopyRotamerMover::set_target_res_index(const unsigned long) –> void

set_template_res_index(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, index_in: int) → None

Set pose index of the residue FROM which we’re copying.

C++: protocols::simple_moves::CopyRotamerMover::set_template_res_index(const unsigned long) –> 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.simple_moves.CopyRotamerMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.CopyRotamerMover, output: pyrosetta.rosetta.std.ostream) -> None

Show the contents of the Mover

C++: protocols::simple_moves::CopyRotamerMover::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.simple_moves.CoupledMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover is called by CoupledMovesProtocol to make a single coupled 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.simple_moves.CoupledMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_task: pyrosetta.rosetta.core.pack.task.PackerTask, ligand_resnum: int) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, arg0: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) -> 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.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CoupledMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, : pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.simple_moves.CoupledMover

C++: protocols::simple_moves::CoupledMover::operator=(const class protocols::simple_moves::CoupledMover &) –> class protocols::simple_moves::CoupledMover &

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.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::simple_moves::CoupledMover::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.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::simple_moves::CoupledMover::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_bias_sampling(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool

C++: protocols::simple_moves::CoupledMover::get_bias_sampling() const –> bool

get_bump_check(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool

C++: protocols::simple_moves::CoupledMover::get_bump_check() const –> bool

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_fix_backbone(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool

C++: protocols::simple_moves::CoupledMover::get_fix_backbone() const –> bool

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_ligand_jump_id(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int

C++: protocols::simple_moves::CoupledMover::get_ligand_jump_id() const –> unsigned long

get_ligand_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int

C++: protocols::simple_moves::CoupledMover::get_ligand_resnum() const –> unsigned long

get_ligand_weight(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float

C++: protocols::simple_moves::CoupledMover::get_ligand_weight() const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → str

C++: protocols::simple_moves::CoupledMover::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_packer_task(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::simple_moves::CoupledMover::get_packer_task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

get_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool

C++: protocols::simple_moves::CoupledMover::get_randomize_resnum() const –> bool

get_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → int

C++: protocols::simple_moves::CoupledMover::get_resnum() const –> unsigned long

get_rigid_body_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover

C++: protocols::simple_moves::CoupledMover::get_rigid_body_mover() const –> class std::shared_ptr<class protocols::rigid::RigidBodyPerturbMover>

get_rotation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float

C++: protocols::simple_moves::CoupledMover::get_rotation_magnitude() const –> double

get_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float

C++: protocols::simple_moves::CoupledMover::get_rotation_std_dev() const –> double

get_score_fxn(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::CoupledMover::get_score_fxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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_short_backrub_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover

C++: protocols::simple_moves::CoupledMover::get_short_backrub_mover() const –> class std::shared_ptr<class protocols::simple_moves::ShortBackrubMover>

get_temperature(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float

C++: protocols::simple_moves::CoupledMover::get_temperature() const –> double

get_translation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → float

C++: protocols::simple_moves::CoupledMover::get_translation_magnitude() const –> double

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

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

get_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover) → bool

C++: protocols::simple_moves::CoupledMover::get_uniform_backrub() const –> bool

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

mover_name() → str

C++: protocols::simple_moves::CoupledMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::CoupledMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_bias_sampling(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, bias_sampling: bool) → None

C++: protocols::simple_moves::CoupledMover::set_bias_sampling(bool) –> void

set_bump_check(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, bump_check: bool) → None

C++: protocols::simple_moves::CoupledMover::set_bump_check(bool) –> 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_fix_backbone(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, fix_backbone: bool) → None

C++: protocols::simple_moves::CoupledMover::set_fix_backbone(bool) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

set_ligand_jump_id(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_jump_id: int) → None

C++: protocols::simple_moves::CoupledMover::set_ligand_jump_id(unsigned long) –> void

set_ligand_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_resnum: int, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CoupledMover::set_ligand_resnum(unsigned long, class std::shared_ptr<const class core::pose::Pose>) –> void

set_ligand_weight(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, ligand_weight: float) → None

C++: protocols::simple_moves::CoupledMover::set_ligand_weight(double) –> 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_randomize_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, randomize_resnum: bool) → None

C++: protocols::simple_moves::CoupledMover::set_randomize_resnum(bool) –> void

set_resnum(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, resnum: int) → None

C++: protocols::simple_moves::CoupledMover::set_resnum(unsigned long) –> void

set_rigid_body_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rigid_body_mover: pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover) → None

C++: protocols::simple_moves::CoupledMover::set_rigid_body_mover(class std::shared_ptr<class protocols::rigid::RigidBodyPerturbMover>) –> void

set_rotation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rotation_magnitude: float) → None

C++: protocols::simple_moves::CoupledMover::set_rotation_magnitude(double) –> void

set_rotation_std_dev(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, rotation_std_dev: float) → None

C++: protocols::simple_moves::CoupledMover::set_rotation_std_dev(double) –> void

set_score_fxn(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::CoupledMover::set_score_fxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_short_backrub_mover(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, short_backrub_mover: pyrosetta.rosetta.protocols.simple_moves.ShortBackrubMover) → None

C++: protocols::simple_moves::CoupledMover::set_short_backrub_mover(class std::shared_ptr<class protocols::simple_moves::ShortBackrubMover>) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, temperature: float) → None

C++: protocols::simple_moves::CoupledMover::set_temperature(double) –> void

set_translation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, translation_magnitude: float) → None

C++: protocols::simple_moves::CoupledMover::set_translation_magnitude(double) –> 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

set_uniform_backrub(self: pyrosetta.rosetta.protocols.simple_moves.CoupledMover, uniform_backrub: bool) → None

C++: protocols::simple_moves::CoupledMover::set_uniform_backrub(bool) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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.simple_moves.CstInfoMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A Mover to output information about constraints

__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.simple_moves.CstInfoMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, arg0: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) → str

__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).

add_info_for_csts(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, cstlist: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) → None

C++: protocols::simple_moves::CstInfoMover::add_info_for_csts(const class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > > &, class core::pose::Pose &, const class std::basic_string<char> &) const –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CstInfoMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, : pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) → pyrosetta.rosetta.protocols.simple_moves.CstInfoMover

C++: protocols::simple_moves::CstInfoMover::operator=(const class protocols::simple_moves::CstInfoMover &) –> class protocols::simple_moves::CstInfoMover &

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.simple_moves.CstInfoMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CstInfoMover::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>

cst_file(*args, **kwargs)

Overloaded function.

1. cst_file(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, setting: str) -> None

C++: protocols::simple_moves::CstInfoMover::cst_file(const class std::basic_string<char> &) –> void

2. cst_file(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) -> str

C++: protocols::simple_moves::CstInfoMover::cst_file() const –> const std::string &

dump_cst_file(*args, **kwargs)

Overloaded function.

1. dump_cst_file(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, setting: str) -> None

C++: protocols::simple_moves::CstInfoMover::dump_cst_file(const class std::basic_string<char> &) –> void

2. dump_cst_file(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) -> str

C++: protocols::simple_moves::CstInfoMover::dump_cst_file() const –> const std::string &

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

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::CstInfoMover::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_constraints_from_file(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, filename: str, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::simple_moves::CstInfoMover::get_constraints_from_file(const class std::basic_string<char> &, const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

get_constraints_from_pose(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

C++: protocols::simple_moves::CstInfoMover::get_constraints_from_pose(const class core::pose::Pose &) const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

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.simple_moves.CstInfoMover) → str

C++: protocols::simple_moves::CstInfoMover::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

mover_name() → str

C++: protocols::simple_moves::CstInfoMover::mover_name() –> std::string

name() → str

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

prefix(*args, **kwargs)

Overloaded function.

1. prefix(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, setting: str) -> None

C++: protocols::simple_moves::CstInfoMover::prefix(const class std::basic_string<char> &) –> void

2. prefix(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) -> str

C++: protocols::simple_moves::CstInfoMover::prefix() const –> const std::string &

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::CstInfoMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recursive(*args, **kwargs)

Overloaded function.

1. recursive(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover, setting: bool) -> None

C++: protocols::simple_moves::CstInfoMover::recursive(bool) –> void

2. recursive(self: pyrosetta.rosetta.protocols.simple_moves.CstInfoMover) -> bool

C++: protocols::simple_moves::CstInfoMover::recursive() const –> bool

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

C++: protocols::simple_moves::CstInfoMover::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.simple_moves.CutChainMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

simple mover that sperates Fv from Fl into two seperate chains

__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.simple_moves.CutChainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) -> 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.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CutChainMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → pyrosetta.rosetta.protocols.simple_moves.CutChainMover

C++: protocols::simple_moves::CutChainMover::operator=(const class protocols::simple_moves::CutChainMover &) –> class protocols::simple_moves::CutChainMover &

bond_length(*args, **kwargs)

Overloaded function.

1. bond_length(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) -> float

C++: protocols::simple_moves::CutChainMover::bond_length() const –> double

2. bond_length(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : float) -> None

C++: protocols::simple_moves::CutChainMover::bond_length(const double) –> void

chain_cut(*args, **kwargs)

Overloaded function.

1. chain_cut(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::simple_moves::CutChainMover::chain_cut(class core::pose::Pose &) –> unsigned long

2. chain_cut(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int) -> int

C++: protocols::simple_moves::CutChainMover::chain_cut(class core::pose::Pose &, unsigned long, unsigned long) –> unsigned long

chain_id(*args, **kwargs)

Overloaded function.

1. chain_id(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) -> int

C++: protocols::simple_moves::CutChainMover::chain_id() const –> unsigned long

2. chain_id(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, : int) -> None

C++: protocols::simple_moves::CutChainMover::chain_id(const unsigned long) –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover) → pyrosetta.rosetta.protocols.moves.Mover

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

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

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

create_subpose(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CutChainMover::create_subpose(class core::pose::Pose &) –> void

foldTree(self: pyrosetta.rosetta.protocols.simple_moves.CutChainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CutChainMover::foldTree(class core::pose::Pose &) –> void

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

C++: protocols::simple_moves::CutChainMover::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.simple_moves.CutChainMover) → str

C++: protocols::simple_moves::CutChainMover::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.simple_moves.CyclizationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover performas a variaty of functions related to cyclizing a chain in a pose.

__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.simple_moves.CyclizationMover, chain_to_cyclize: int, add_constraints: bool, minimize: bool, minimization_rebuild_rounds: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CyclizationMover, chain_to_cyclize: int, add_constraints: bool, minimize: bool, minimization_rebuild_rounds: int, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction, move_map: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.CyclizationMover, arg0: pyrosetta.rosetta.protocols.simple_moves.CyclizationMover) -> 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.simple_moves.CyclizationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::CyclizationMover::apply(class core::pose::Pose &) –> void

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

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

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.simple_moves.CyclizationMover) → str

C++: protocols::simple_moves::CyclizationMover::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.simple_moves.DeleteChainsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Delete a chain from a Pose, or a set of chains.

1. Deletes Each chain using conformation.delete_residue_range_slow

   2. Calls detect bonds, pseudobonds, and disulfides
   3. Makes sure PDBInfo is still intact
   4. Sets a new reasonable FoldTree

__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.simple_moves.DeleteChainsMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, chains: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, chains: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, arg0: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) -> 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.simple_moves.DeleteChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::DeleteChainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, : pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover

C++: protocols::simple_moves::DeleteChainsMover::operator=(const class protocols::simple_moves::DeleteChainsMover &) –> class protocols::simple_moves::DeleteChainsMover &

chains(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get the chain

C++: protocols::simple_moves::DeleteChainsMover::chains() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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.simple_moves.DeleteChainsMover) → pyrosetta.rosetta.protocols.moves.Mover

///////////// Mover Methods /////////////////////////////////////////////

C++: protocols::simple_moves::DeleteChainsMover::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>

detect_bonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → bool

C++: protocols::simple_moves::DeleteChainsMover::detect_bonds() const –> bool

detect_pseudobonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → bool

C++: protocols::simple_moves::DeleteChainsMover::detect_pseudobonds() const –> bool

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

C++: protocols::simple_moves::DeleteChainsMover::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.simple_moves.DeleteChainsMover) → str

C++: protocols::simple_moves::DeleteChainsMover::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

mover_name() → str

C++: protocols::simple_moves::DeleteChainsMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::DeleteChainsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_chains(*args, **kwargs)

Overloaded function.

1. set_chains(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, chains: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

Set the chain

C++: protocols::simple_moves::DeleteChainsMover::set_chains(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. set_chains(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, chains: str, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Set the chain

C++: protocols::simple_moves::DeleteChainsMover::set_chains(const class std::basic_string<char> &, const class core::pose::Pose &) –> 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_defaults(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover) → None

C++: protocols::simple_moves::DeleteChainsMover::set_defaults() –> void

set_detect_bonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, detect_bonds: bool) → None

Set the class to detect bonds after full deletion of chains?

Default True. Override for speed and if you know there are no bonds between chains other than possible disulfides.

C++: protocols::simple_moves::DeleteChainsMover::set_detect_bonds(bool) –> void

set_detect_pseudobonds(self: pyrosetta.rosetta.protocols.simple_moves.DeleteChainsMover, detect_pseudobonds: bool) → None

Set the class to detect psuedobonds after full deletion of chains?

Default True. Override for speed and if you know there are no pseudobonds between chains other than possible disulfides.

C++: protocols::simple_moves::DeleteChainsMover::set_detect_pseudobonds(bool) –> 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.simple_moves.DesignRepackMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a pure virtual base class for movers which redesign and repack the interface

__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.simple_moves.DesignRepackMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, name: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, arg0: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> 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.simple_moves.DesignRepackMover, : pyrosetta.rosetta.core.pose.Pose) → None

a dummy apply so that instantiation of this baseclass would be possible.

C++: protocols::simple_moves::DesignRepackMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, : pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover

C++: protocols::simple_moves::DesignRepackMover::operator=(const class protocols::simple_moves::DesignRepackMover &) –> class protocols::simple_moves::DesignRepackMover &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clear_task(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → None

after fiddling with a task from outside this mover, clear it, or else, on the next iteration through

the mover the changes will be remembered

C++: protocols::simple_moves::DesignRepackMover::clear_task() –> void

clear_task_factory(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → None

C++: protocols::simple_moves::DesignRepackMover::clear_task_factory() –> 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>

design(*args, **kwargs)

Overloaded function.

1. design(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, des: bool) -> None

C++: protocols::simple_moves::DesignRepackMover::design(const bool) –> void

2. design(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> bool

C++: protocols::simple_moves::DesignRepackMover::design() const –> bool

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.simple_moves.DesignRepackMover) → str

C++: protocols::simple_moves::DesignRepackMover::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

get_xsd_complex_type() → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::DesignRepackMover::get_xsd_complex_type() –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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

min_bb(*args, **kwargs)

Overloaded function.

1. min_bb(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, min_bb: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::simple_moves::DesignRepackMover::min_bb(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

2. min_bb(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::simple_moves::DesignRepackMover::min_bb() const –> const class utility::vector1<bool, class std::allocator<bool> > &

min_bb_set(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → bool

C++: protocols::simple_moves::DesignRepackMover::min_bb_set() const –> bool

min_rb(*args, **kwargs)

Overloaded function.

1. min_rb(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, min_rb: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::simple_moves::DesignRepackMover::min_rb(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

2. min_rb(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, min_rb: bool) -> None

in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code.

C++: protocols::simple_moves::DesignRepackMover::min_rb(const bool) –> void

3. min_rb(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::simple_moves::DesignRepackMover::min_rb() const –> const class utility::vector1<bool, class std::allocator<bool> > &

min_rb_set(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → bool

C++: protocols::simple_moves::DesignRepackMover::min_rb_set() const –> bool

min_sc(*args, **kwargs)

Overloaded function.

1. min_sc(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, min_sc: pyrosetta.rosetta.utility.vector1_bool) -> None

C++: protocols::simple_moves::DesignRepackMover::min_sc(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

2. min_sc(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_bool

C++: protocols::simple_moves::DesignRepackMover::min_sc() const –> const class utility::vector1<bool, class std::allocator<bool> > &

min_sc_set(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → bool

C++: protocols::simple_moves::DesignRepackMover::min_sc_set() const –> bool

name() → str

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

optimize_foldtree(*args, **kwargs)

Overloaded function.

1. optimize_foldtree(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> bool

C++: protocols::simple_moves::DesignRepackMover::optimize_foldtree() const –> bool

2. optimize_foldtree(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, opt: bool) -> None

C++: protocols::simple_moves::DesignRepackMover::optimize_foldtree(const bool) –> void

prevent_repacking(*args, **kwargs)

Overloaded function.

1. prevent_repacking(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, p: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::simple_moves::DesignRepackMover::prevent_repacking(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. prevent_repacking(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::DesignRepackMover::prevent_repacking() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

restrict_to_repacking(*args, **kwargs)

Overloaded function.

1. restrict_to_repacking(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, p: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::simple_moves::DesignRepackMover::restrict_to_repacking(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

2. restrict_to_repacking(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::DesignRepackMover::restrict_to_repacking() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

scorefxn_minimize(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::DesignRepackMover::scorefxn_minimize() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

scorefxn_repack(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::DesignRepackMover::scorefxn_repack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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_scorefxn_minimize(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::DesignRepackMover::set_scorefxn_minimize(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_scorefxn_repack(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::DesignRepackMover::set_scorefxn_repack(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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

setup_packer_and_movemap(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap(const 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(class std::basic_ostream<char> &) const –> void

task(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::simple_moves::DesignRepackMover::task() –> class std::shared_ptr<class core::pack::task::PackerTask> &

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, p: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::DesignRepackMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::DesignRepackMover::task_factory() –> class std::shared_ptr<class core::pack::task::TaskFactory> &

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

use_preset_task(*args, **kwargs)

Overloaded function.

1. use_preset_task(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover, bt: bool) -> None

C++: protocols::simple_moves::DesignRepackMover::use_preset_task(const bool) –> void

2. use_preset_task(self: pyrosetta.rosetta.protocols.simple_moves.DesignRepackMover) -> bool

C++: protocols::simple_moves::DesignRepackMover::use_preset_task() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a mover that given a receptor peptide pose mutates the peptides edge residues to cysteins, if needed, and enforces disulfide bonding by constrained minimization of the bond and the interaction

__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.simple_moves.DisulfideInsertionMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, arg0: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) -> 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.simple_moves.DisulfideInsertionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::DisulfideInsertionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, : pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover

C++: protocols::simple_moves::DisulfideInsertionMover::operator=(const class protocols::simple_moves::DisulfideInsertionMover &) –> class protocols::simple_moves::DisulfideInsertionMover &

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.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::DisulfideInsertionMover::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>

determine_cyclization_viability(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, partner_pose: pyrosetta.rosetta.core.pose.Pose, n_cyd_position: int, c_cyd_position: int) → pyrosetta.rosetta.protocols.simple_moves.DisulfideCyclizationViability

checks if two residues in a pose are near enough in space

and geometrically similar enough to existing disulfide forming cys

C++: protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(const class core::pose::Pose &, const unsigned long, unsigned long) –> enum protocols::simple_moves::DisulfideCyclizationViability

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_c_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int

C++: protocols::simple_moves::DisulfideInsertionMover::get_c_cyd_seqpos() const –> unsigned long

get_constraint_weight(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float

C++: protocols::simple_moves::DisulfideInsertionMover::get_constraint_weight() const –> double

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_max_dslf_energy(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float

C++: protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_energy() –> double

get_max_dslf_pot(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → float

C++: protocols::simple_moves::DisulfideInsertionMover::get_max_dslf_pot() –> double

get_movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.core.select.movemap.MoveMapFactory

C++: protocols::simple_moves::DisulfideInsertionMover::get_movemap_factory() const –> class std::shared_ptr<const class core::select::movemap::MoveMapFactory>

get_n_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int

C++: protocols::simple_moves::DisulfideInsertionMover::get_n_cyd_seqpos() const –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → str

C++: protocols::simple_moves::DisulfideInsertionMover::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_peptide_chain(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → int

C++: protocols::simple_moves::DisulfideInsertionMover::get_peptide_chain() const –> unsigned long

get_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::DisulfideInsertionMover::get_scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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

mover_name() → str

C++: protocols::simple_moves::DisulfideInsertionMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::DisulfideInsertionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_c_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, c_cyd_seqpos: int) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_c_cyd_seqpos(const unsigned long) –> void

set_constraint_weight(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_constraint_weight(const double) –> 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_max_dslf_energy(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_energy(const double) –> void

set_max_dslf_pot(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: float) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_max_dslf_pot(const double) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, mm: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_movemap_factory(const class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

set_n_cyd_seqpos(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, n_cyd_seqpos: int) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_n_cyd_seqpos(const unsigned long) –> 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_peptide_chain(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, value: int) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_peptide_chain(const unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DisulfideInsertionMover, score_function: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::DisulfideInsertionMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.simple_moves.DumpPdb

Bases: pyrosetta.rosetta.protocols.moves.Mover

what you think this can now be assimilated into DumpPdbMover

__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.simple_moves.DumpPdb) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, fname: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, arg0: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) -> 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.simple_moves.DumpPdb, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::DumpPdb::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, : pyrosetta.rosetta.protocols.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.simple_moves.DumpPdb

C++: protocols::simple_moves::DumpPdb::operator=(const class protocols::simple_moves::DumpPdb &) –> class protocols::simple_moves::DumpPdb &

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.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::DumpPdb::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.simple_moves.DumpPdb) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::DumpPdb::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.simple_moves.DumpPdb) → str

C++: protocols::simple_moves::DumpPdb::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

mover_name() → str

C++: protocols::simple_moves::DumpPdb::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::DumpPdb::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_filename(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, filename_in: str) → None

Set the filename for writing.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::DumpPdb::set_filename(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_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::DumpPdb::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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

tag_time(*args, **kwargs)

Overloaded function.

1. tag_time(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb, setting: bool) -> None

C++: protocols::simple_moves::DumpPdb::tag_time(bool) –> void

2. tag_time(self: pyrosetta.rosetta.protocols.simple_moves.DumpPdb) -> bool

C++: protocols::simple_moves::DumpPdb::tag_time() const –> bool

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

Given a residue index, dump all of the rotamers to individual PDB files within 0-1 sd of the mean

__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.simple_moves.DumpSingleResidueRotamers) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, rsd_index: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, arg0: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → str

__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.simple_moves.DumpSingleResidueRotamers, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the mover

C++: protocols::simple_moves::DumpSingleResidueRotamers::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers, : pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.simple_moves.DumpSingleResidueRotamers

C++: protocols::simple_moves::DumpSingleResidueRotamers::operator=(const class protocols::simple_moves::DumpSingleResidueRotamers &) –> class protocols::simple_moves::DumpSingleResidueRotamers &

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.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::DumpSingleResidueRotamers::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.simple_moves.DumpSingleResidueRotamers) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::DumpSingleResidueRotamers::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.simple_moves.DumpSingleResidueRotamers) → str

C++: protocols::simple_moves::DumpSingleResidueRotamers::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

mover_name() → str

C++: protocols::simple_moves::DumpSingleResidueRotamers::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::DumpSingleResidueRotamers::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

C++: protocols::simple_moves::DumpSingleResidueRotamers::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.simple_moves.EnergyCutRotamerTrialsMinMover

Bases: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover

Wrapper for Rotamer Trials with Minimization, which modifies only rotamers whose energy changed by a given constant

__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.simple_moves.EnergyCutRotamerTrialsMinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, task_in: pyrosetta.rosetta.core.pack.task.PackerTask, mc_in: pyrosetta.rosetta.protocols.moves.MonteCarlo, energycut_in: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, factory_in: pyrosetta.rosetta.core.pack.task.TaskFactory, mc_in: pyrosetta.rosetta.protocols.moves.MonteCarlo, energycut_in: float) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover) → str

__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.simple_moves.EnergyCutRotamerTrialsMinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply this mover to a pose

C++: protocols::simple_moves::EnergyCutRotamerTrialsMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover, : pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover) → pyrosetta.rosetta.protocols.simple_moves.EnergyCutRotamerTrialsMinMover

C++: protocols::simple_moves::EnergyCutRotamerTrialsMinMover::operator=(const class protocols::simple_moves::EnergyCutRotamerTrialsMinMover &) –> class protocols::simple_moves::EnergyCutRotamerTrialsMinMover &

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.simple_moves.RotamerTrialsMinMover) → pyrosetta.rosetta.protocols.moves.Mover

Return a copy of this mover instance (for RosettaScripts)

C++: protocols::simple_moves::RotamerTrialsMinMover::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.simple_moves.RotamerTrialsMinMover) → pyrosetta.rosetta.protocols.moves.Mover

Return a new mover instance (for RosettaScripts)

C++: protocols::simple_moves::RotamerTrialsMinMover::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.simple_moves.EnergyCutRotamerTrialsMinMover) → str

C++: protocols::simple_moves::EnergyCutRotamerTrialsMinMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover) → None

C++: protocols::simple_moves::RotamerTrialsMinMover::init() –> void

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

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

mover_name() → str

C++: protocols::simple_moves::RotamerTrialsMinMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::RotamerTrialsMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

score_function(self: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::RotamerTrialsMinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.simple_moves.RotamerTrialsMinMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover, output: pyrosetta.rosetta.std.ostream) -> None

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

task_factory(self: pyrosetta.rosetta.protocols.simple_moves.RotamerTrialsMinMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) → None

C++: protocols::simple_moves::RotamerTrialsMinMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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.simple_moves.ForceDisulfidesMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

simple mover that fixes disulfides according to a defined list and then simultaneously repacks within 6A shells around each affected cystein residue.

__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.simple_moves.ForceDisulfidesMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover) -> 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.simple_moves.ForceDisulfidesMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ForceDisulfidesMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover, : pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover) → pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover

C++: protocols::simple_moves::ForceDisulfidesMover::operator=(const class protocols::simple_moves::ForceDisulfidesMover &) –> class protocols::simple_moves::ForceDisulfidesMover &

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.simple_moves.ForceDisulfidesMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ForceDisulfidesMover::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>

disulfides(*args, **kwargs)

Overloaded function.

1. disulfides(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover, : pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> None

C++: protocols::simple_moves::ForceDisulfidesMover::disulfides(class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >) –> void

2. disulfides(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::simple_moves::ForceDisulfidesMover::disulfides() const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

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

C++: protocols::simple_moves::ForceDisulfidesMover::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.simple_moves.ForceDisulfidesMover) → str

C++: protocols::simple_moves::ForceDisulfidesMover::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

mover_name() → str

C++: protocols::simple_moves::ForceDisulfidesMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ForceDisulfidesMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::ForceDisulfidesMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

2. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.ForceDisulfidesMover, s: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::ForceDisulfidesMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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.simple_moves.FragmentMover

Bases: pyrosetta.rosetta.protocols.moves.MoveMapMover

abstract base class for FragmentMovers

__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.simple_moves.FragmentMover, arg0: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → 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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None
2. apply(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool

apply a fragment at pos to movemable dofs

C++: protocols::simple_moves::FragmentMover::apply(class core::pose::Pose &, unsigned long) const –> bool

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

assign(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.protocols.simple_moves.FragmentMover

C++: protocols::simple_moves::FragmentMover::operator=(const class protocols::simple_moves::FragmentMover &) –> class protocols::simple_moves::FragmentMover &

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>

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

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

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.simple_moves.FragmentMover) → str

C++: protocols::simple_moves::FragmentMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

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_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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.simple_moves.GenericSimulatedAnnealer

Bases: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover

GenericSimulatedAnnealer mover for performing simulated annealing trajectories

This class extends GenericMonteCarloMover to provide temperature scaling

__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.simple_moves.GenericSimulatedAnnealer) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, arg0: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) -> 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).

accept(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, provisional_scores: pyrosetta.rosetta.utility.vector1_double, mca_status: pyrosetta.rosetta.protocols.moves.MCA) → None

Does what the mover needs to do when a pose is accepted, given a pose and scores

C++: protocols::simple_moves::GenericMonteCarloMover::accept(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &, const enum protocols::moves::MCA) –> void

accept_counter(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → int

C++: protocols::simple_moves::GenericMonteCarloMover::accept_counter() const –> unsigned long

accepted_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, i: int) → pyrosetta.rosetta.protocols.simple_moves.AcceptedScores

gets a list of scores for acceptance number i

C++: protocols::simple_moves::GenericSimulatedAnnealer::accepted_scores(const unsigned long) const –> const class protocols::simple_moves::AcceptedScores &

adaptation_period(*args, **kwargs)

Overloaded function.

1. adaptation_period(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, a: int) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::adaptation_period(const unsigned long) –> void

2. adaptation_period(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> int

C++: protocols::simple_moves::GenericMonteCarloMover::adaptation_period() const –> unsigned long

adaptive(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_bool

C++: protocols::simple_moves::GenericMonteCarloMover::adaptive() const –> const class utility::vector1<bool, class std::allocator<bool> > &

adaptive_movers(*args, **kwargs)

Overloaded function.

1. adaptive_movers(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, a: bool) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::adaptive_movers(const bool) –> void

2. adaptive_movers(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> bool

C++: protocols::simple_moves::GenericMonteCarloMover::adaptive_movers() const –> bool

add_filter(*args, **kwargs)

Overloaded function.

1. add_filter(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str) -> None
2. add_filter(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter, adaptive: bool, temp: float, sample_type: str, rank_by: bool) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const bool, const double, const class std::basic_string<char> &, bool) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → None

apply GenericSimulatedAnnealer (Mover)

C++: protocols::simple_moves::GenericSimulatedAnnealer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, : pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer

C++: protocols::simple_moves::GenericSimulatedAnnealer::operator=(const class protocols::simple_moves::GenericSimulatedAnnealer &) –> class protocols::simple_moves::GenericSimulatedAnnealer &

boltz_rank(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → bool

C++: protocols::simple_moves::GenericMonteCarloMover::boltz_rank() const –> bool

boltzmann(*args, **kwargs)

Overloaded function.

1. boltzmann(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

core of MC

C++: protocols::simple_moves::GenericMonteCarloMover::boltzmann(class core::pose::Pose &) –> bool

2. boltzmann(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) -> bool

core of MC – evaulates a pose based on the scores/filters + temperatures. random_num is a vector of random numbers between 0 and 1 with size equal to the number of MC criteria

C++: protocols::simple_moves::GenericMonteCarloMover::boltzmann(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> bool

boltzmann_result(*args, **kwargs)

Overloaded function.

1. boltzmann_result(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.protocols.simple_moves.TrialResult

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

uses randomly generated numbers to assess acceptance of scores with temperatures

C++: protocols::simple_moves::GenericSimulatedAnnealer::boltzmann_result(class core::pose::Pose &) –> enum protocols::simple_moves::TrialResult

2. boltzmann_result(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose, random_nums: pyrosetta.rosetta.utility.vector1_double) -> pyrosetta.rosetta.protocols.simple_moves.TrialResult

given a modified pose, determines whether we should accept or not, and updates internal class data accordingly

C++: protocols::simple_moves::GenericSimulatedAnnealer::boltzmann_result(class core::pose::Pose &, const class utility::vector1<double, class std::allocator<double> > &) –> enum protocols::simple_moves::TrialResult

calc_boltz_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, scores: pyrosetta.rosetta.utility.vector1_double) → float

if boltz_rank is used, this will calculate the ranking score from a list of filter scores

C++: protocols::simple_moves::GenericSimulatedAnnealer::calc_boltz_score(const class utility::vector1<double, class std::allocator<double> > &) const –> double

checkpoint_exists(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → bool

tests to see if the checkpoint files exist and have been generated

C++: protocols::simple_moves::GenericSimulatedAnnealer::checkpoint_exists() const –> bool

checkpoint_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, check_file: str) → None

set the checkpoint file name

C++: protocols::simple_moves::GenericSimulatedAnnealer::checkpoint_file(const class std::basic_string<char> &) –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → pyrosetta.rosetta.protocols.moves.Mover

create copy constructor

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

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

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

create_tag(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, suffix: str) → str

create a silent struct tag for checkpointing with the given suffix

C++: protocols::simple_moves::GenericSimulatedAnnealer::create_tag(const class std::basic_string<char> &) const –> std::string

current_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → float

return the lowest score

C++: protocols::simple_moves::GenericMonteCarloMover::current_score() const –> double

define_composition_schema(: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::GenericMonteCarloMover::define_composition_schema(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

drift(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → bool

C++: protocols::simple_moves::GenericMonteCarloMover::drift() const –> bool

filters(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t

C++: protocols::simple_moves::GenericMonteCarloMover::filters() const –> const class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > > &

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

create this type of objectt

C++: protocols::simple_moves::GenericSimulatedAnnealer::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.simple_moves.GenericSimulatedAnnealer) → str

C++: protocols::simple_moves::GenericSimulatedAnnealer::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 > > &

initialize(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → None

initialize object used in constructor

C++: protocols::simple_moves::GenericMonteCarloMover::initialize() –> void

keep_checkpoint_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, keep_checkpoint: bool) → None

sets whether or not to delete checkpoint files when done – useful for debugging

C++: protocols::simple_moves::GenericSimulatedAnnealer::keep_checkpoint_file(const bool) –> void

keep_filters(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → bool

C++: protocols::simple_moves::GenericMonteCarloMover::keep_filters() const –> bool

last_accepted_pose(*args, **kwargs)

Overloaded function.

1. last_accepted_pose(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the last accepted pose

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose() const –> class std::shared_ptr<class core::pose::Pose>

2. last_accepted_pose(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_pose(class std::shared_ptr<class core::pose::Pose>) –> void

last_accepted_score(*args, **kwargs)

Overloaded function.

1. last_accepted_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> float

return the last accepted score

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_score() const –> double

2. last_accepted_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, score: float) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_score(const double) –> void

last_accepted_scores(*args, **kwargs)

Overloaded function.

1. last_accepted_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

2. last_accepted_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::last_accepted_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

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

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

last_tested_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::simple_moves::GenericMonteCarloMover::last_tested_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

load_checkpoint_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → None

loads checkpoint data and attempts to resume a run with pose as the pose

C++: protocols::simple_moves::GenericSimulatedAnnealer::load_checkpoint_file(class core::pose::Pose &) –> void

load_trial_number_from_checkpoint(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, : pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::simple_moves::GenericMonteCarloMover::load_trial_number_from_checkpoint(class core::pose::Pose &) –> unsigned long

lowest_score(*args, **kwargs)

Overloaded function.

1. lowest_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> float

return the lowest score

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_score() const –> double

2. lowest_score(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, score: float) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_score(const double) –> void

lowest_score_pose(*args, **kwargs)

Overloaded function.

1. lowest_score_pose(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pose.Pose

return the lowest score pose

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_score_pose() const –> class std::shared_ptr<class core::pose::Pose>

2. lowest_score_pose(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_score_pose(class std::shared_ptr<class core::pose::Pose>) –> void

lowest_scores(*args, **kwargs)

Overloaded function.

1. lowest_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_scores() const –> const class utility::vector1<double, class std::allocator<double> > &

2. lowest_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, scores: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::lowest_scores(const class utility::vector1<double, class std::allocator<double> > &) –> void

max_accepted_trials(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → int

Returns maximum number of accepted trials

C++: protocols::simple_moves::GenericMonteCarloMover::max_accepted_trials() const –> unsigned long

maxtrials(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → int

Returns maximum number of trials

C++: protocols::simple_moves::GenericMonteCarloMover::maxtrials() const –> unsigned long

mc_accpeted(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.MCA

return mc_accepted

C++: protocols::simple_moves::GenericMonteCarloMover::mc_accpeted() const –> enum protocols::moves::MCA

mover(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::GenericMonteCarloMover::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

mover_name() → str

C++: protocols::simple_moves::GenericSimulatedAnnealer::mover_name() –> std::string

name() → str

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

num_accepted_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → int

number of acceptances

C++: protocols::simple_moves::GenericSimulatedAnnealer::num_accepted_scores() const –> unsigned long

num_designable(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → int

C++: protocols::simple_moves::GenericMonteCarloMover::num_designable(class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask> &) –> unsigned long

num_rejections(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::GenericMonteCarloMover::num_rejections() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

num_triggers(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → int

Returns the number of triggers

C++: protocols::simple_moves::GenericMonteCarloMover::num_triggers() const –> unsigned long

preapply(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → bool

C++: protocols::simple_moves::GenericMonteCarloMover::preapply() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::GenericSimulatedAnnealer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

recover_low(*args, **kwargs)

Overloaded function.

1. recover_low(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None

return the simulation state to the lowest energy structure we’ve seen

C++: protocols::simple_moves::GenericMonteCarloMover::recover_low(class core::pose::Pose &) –> void

2. recover_low(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> bool

C++: protocols::simple_moves::GenericMonteCarloMover::recover_low() const –> bool

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

remove_checkpoint_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → None

Deletes the checkpoint files

C++: protocols::simple_moves::GenericSimulatedAnnealer::remove_checkpoint_file() const –> void

remove_trigger(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, trigger_id: int) → None

Removes the trigger with the specified id

C++: protocols::simple_moves::GenericMonteCarloMover::remove_trigger(unsigned long) –> void

reset(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → None

Clears accepted data and initialize with new pose

C++: protocols::simple_moves::GenericSimulatedAnnealer::reset(class core::pose::Pose &) –> void

reset_baselines(*args, **kwargs)

Overloaded function.

1. reset_baselines(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, r: bool) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::reset_baselines(const bool) –> void

2. reset_baselines(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> bool

C++: protocols::simple_moves::GenericMonteCarloMover::reset_baselines() 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

sample_types(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::simple_moves::GenericMonteCarloMover::sample_types() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

save_checkpoint_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer) → None

Saves the current state of the mover into checkpoint files

C++: protocols::simple_moves::GenericSimulatedAnnealer::save_checkpoint_file() const –> void

save_trial_number_to_checkpoint(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, i: int) → None

C++: protocols::simple_moves::GenericMonteCarloMover::save_trial_number_to_checkpoint(const unsigned long) const –> void

saved_accept_file_name(*args, **kwargs)

Overloaded function.

1. saved_accept_file_name(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> str

C++: protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name() const –> std::string

2. saved_accept_file_name(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, : str) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::saved_accept_file_name(const class std::basic_string<char>) –> void

saved_trial_number_file(*args, **kwargs)

Overloaded function.

1. saved_trial_number_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> str

C++: protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file() const –> std::string

2. saved_trial_number_file(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, : str) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::saved_trial_number_file(const class std::basic_string<char>) –> void

scale_temperatures(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, temp_factor: float) → None

scales temperatures by the factor provided

C++: protocols::simple_moves::GenericSimulatedAnnealer::scale_temperatures(const double) –> void

score_function(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

Return the score function in use

C++: protocols::simple_moves::GenericMonteCarloMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

score_pose(self: pyrosetta.rosetta.protocols.simple_moves.GenericSimulatedAnnealer, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.protocols.simple_moves.AcceptedScores

given a pose, score the result

C++: protocols::simple_moves::GenericSimulatedAnnealer::score_pose(const class core::pose::Pose &) const –> class protocols::simple_moves::AcceptedScores

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::GenericMonteCarloMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_boltz_rank(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, boltz_rank: bool) → None

if boltz_rank=true, rank structures by the temperature-weighted

sum of scores, rather than a single filter

The score used here is the effective combined energy function that the Monte Carlo sampler is sampling over.

C++: protocols::simple_moves::GenericMonteCarloMover::set_boltz_rank(const bool) –> 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_drift(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, drift: bool) → None

if drift=false, the pose is set back to the initial pose at each MC trial

Of course, this is not MC sampling.

C++: protocols::simple_moves::GenericMonteCarloMover::set_drift(const bool) –> 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_keep_filters(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, k: bool) → None

C++: protocols::simple_moves::GenericMonteCarloMover::set_keep_filters(const bool) –> void

set_max_accepted_trials(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, n_max_accepted_trial: int) → None

set max accepted trials of MC trials

C++: protocols::simple_moves::GenericMonteCarloMover::set_max_accepted_trials(const unsigned long) –> void

set_maxtrials(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, ntrial: int) → None

set max trials of MC trials

C++: protocols::simple_moves::GenericMonteCarloMover::set_maxtrials(const unsigned long) –> void

set_mover(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, mover: pyrosetta.rosetta.protocols.moves.Mover) → None

set mover

C++: protocols::simple_moves::GenericMonteCarloMover::set_mover(class std::shared_ptr<class protocols::moves::Mover>) –> 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_preapply(*args, **kwargs)

Overloaded function.

1. set_preapply(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> None
2. set_preapply(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, preapply: bool) -> None

if preapply=true, auto-accept the first application of the submover,

ignoring boltzman criteria.

C++: protocols::simple_moves::GenericMonteCarloMover::set_preapply(const bool) –> void

set_recover_low(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, recover_low: bool) → None

if recover_low=true, after apply() the structure

is the lowest energy structure, rather than the last accepted structure.

C++: protocols::simple_moves::GenericMonteCarloMover::set_recover_low(const bool) –> void

set_sampletype(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, type: str) → None

set sample type, max or min

when sample_type == max, sample pose which have higher score when sample_type == min, sample pose which have lower score

C++: protocols::simple_moves::GenericMonteCarloMover::set_sampletype(const class std::basic_string<char> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Pose is evaluated by ScoreFunctionOP during MC trials

C++: protocols::simple_moves::GenericMonteCarloMover::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction> &) –> void

set_stop_sampling(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, stop_sampling: bool) → None

if set to true, the MC mover will stop sampling

C++: protocols::simple_moves::GenericMonteCarloMover::set_stop_sampling(const bool) –> void

set_task_scaling(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, scaling: int) → None

set task multiplier to calculate trials from task

C++: protocols::simple_moves::GenericMonteCarloMover::set_task_scaling(const unsigned long) –> void

set_temperature(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, temp: float) → None

set temperature

C++: protocols::simple_moves::GenericMonteCarloMover::set_temperature(const double) –> 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

show_counters(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None

show counters of ntrial and acceptance ratio

C++: protocols::simple_moves::GenericMonteCarloMover::show_counters(class std::basic_ostream<char> &) const –> void

show_scores(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, out: pyrosetta.rosetta.std.ostream) → None

show scores of last_accepted_score and “best_score” ( = flip_sign_ * lowest_score )

C++: protocols::simple_moves::GenericMonteCarloMover::show_scores(class std::basic_ostream<char> &) const –> void

stop_sampling(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → bool

C++: protocols::simple_moves::GenericMonteCarloMover::stop_sampling() const –> bool

stopping_condition(*args, **kwargs)

Overloaded function.

1. stopping_condition(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, filter: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

2. stopping_condition(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::simple_moves::GenericMonteCarloMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::GenericMonteCarloMover::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

task_scaling(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) → int

Returns the task scaling value

C++: protocols::simple_moves::GenericMonteCarloMover::task_scaling() const –> unsigned long

temperatures(*args, **kwargs)

Overloaded function.

1. temperatures(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::simple_moves::GenericMonteCarloMover::temperatures() const –> class utility::vector1<double, class std::allocator<double> >

2. temperatures(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, temps: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::temperatures(const class utility::vector1<double, class std::allocator<double> > &) –> 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

trial_counter(*args, **kwargs)

Overloaded function.

1. trial_counter(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover) -> int

C++: protocols::simple_moves::GenericMonteCarloMover::trial_counter() const –> unsigned long

2. trial_counter(self: pyrosetta.rosetta.protocols.simple_moves.GenericMonteCarloMover, i: int) -> None

C++: protocols::simple_moves::GenericMonteCarloMover::trial_counter(const unsigned long) –> 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.simple_moves.GroupDiscriminator

Bases: pybind11_builtins.pybind11_object

Interface class used to break a pose down into a set of component “groups” where intra-group rotamer-pair energies are preserved between calls to the GreenPacker. E.g. in rigid-body docking between two proteins, chains 1 and 2 define groups 1 and 2. In rigid-body docking between two domains of the same chain, those residues upstream of jump 1 define group 1, and those downstream of jump 1 define group 2. In loop modelling, the static background is group 1, and the loop itself is group 0, since loop residues will have their bb dofs change regularly between repackings.

__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.simple_moves.GroupDiscriminator) → 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.simple_moves.GroupDiscriminator, : pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator) → pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator

C++: protocols::simple_moves::GroupDiscriminator::operator=(const class protocols::simple_moves::GroupDiscriminator &) –> class protocols::simple_moves::GroupDiscriminator &

clone(self: pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator) → pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator

C++: protocols::simple_moves::GroupDiscriminator::clone() const –> class std::shared_ptr<class protocols::simple_moves::GroupDiscriminator>

group_id(self: pyrosetta.rosetta.protocols.simple_moves.GroupDiscriminator, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) → int

C++: protocols::simple_moves::GroupDiscriminator::group_id(const class core::pose::Pose &, unsigned long) const –> unsigned long

class pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This BS class exists to route around a hard-coded pseudo-Mover in the APPLY_TO_POSE section of the Parser. At XRW2 we needed to move junk out of Parser to use the protocols::moves::MoverFactory instead.

__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.simple_moves.LoadUnboundRotMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover, arg0: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) -> 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.simple_moves.LoadUnboundRotMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::LoadUnboundRotMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover, : pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.simple_moves.LoadUnboundRotMover

C++: protocols::simple_moves::LoadUnboundRotMover::operator=(const class protocols::simple_moves::LoadUnboundRotMover &) –> class protocols::simple_moves::LoadUnboundRotMover &

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.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::LoadUnboundRotMover::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.simple_moves.LoadUnboundRotMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::LoadUnboundRotMover::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.simple_moves.LoadUnboundRotMover) → str

C++: protocols::simple_moves::LoadUnboundRotMover::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

mover_name() → str

C++: protocols::simple_moves::LoadUnboundRotMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::LoadUnboundRotMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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.simple_moves.MembraneTopology

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to change one torsion angle

__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.simple_moves.MembraneTopology) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, arg0: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) -> 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.simple_moves.MembraneTopology, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::MembraneTopology::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, : pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.simple_moves.MembraneTopology

C++: protocols::simple_moves::MembraneTopology::operator=(const class protocols::simple_moves::MembraneTopology &) –> class protocols::simple_moves::MembraneTopology &

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.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::MembraneTopology::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.simple_moves.MembraneTopology) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::MembraneTopology::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.simple_moves.MembraneTopology) → str

C++: protocols::simple_moves::MembraneTopology::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

mover_name() → str

C++: protocols::simple_moves::MembraneTopology::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::MembraneTopology::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

span_file(*args, **kwargs)

Overloaded function.

1. span_file(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology) -> str

C++: protocols::simple_moves::MembraneTopology::span_file() const –> std::string

2. span_file(self: pyrosetta.rosetta.protocols.simple_moves.MembraneTopology, s: str) -> None

C++: protocols::simple_moves::MembraneTopology::span_file(const class std::basic_string<char> &) –> 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.simple_moves.MinMover

Bases: pyrosetta.rosetta.protocols.moves.MoveMapMover

A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set.

Common Methods:

MinMover.apply MinMover.movemap MinMover.score_function

__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.simple_moves.MinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, arg0: pyrosetta.rosetta.core.kinematics.MoveMap, arg1: pyrosetta.rosetta.core.scoring.ScoreFunction, arg2: str, arg3: float, arg4: bool) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, arg0: pyrosetta.rosetta.core.kinematics.MoveMap, arg1: pyrosetta.rosetta.core.scoring.ScoreFunction, arg2: str, arg3: float, arg4: bool, arg5: bool) -> None

doc

5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, min_type_in: str, tolerance_in: float, use_nb_list_in: bool, deriv_check_in: bool, deriv_check_verbose_in: bool) -> None
6. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) → str

__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).

abs_score_convergence_threshold(*args, **kwargs)

Overloaded function.

1. abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, newval: float) -> None

C++: protocols::simple_moves::MinMover::abs_score_convergence_threshold(double) –> void

2. abs_score_convergence_threshold(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> float

C++: protocols::simple_moves::MinMover::abs_score_convergence_threshold() const –> double

abs_score_diff_after_minimization(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) → float

C++: protocols::simple_moves::MinMover::abs_score_diff_after_minimization() const –> double

apply(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Minimizes the DOFs of <pose_> specified in the MoveMap

using the ScoreFunction

example(s):

minmover.apply(pose)

See also:

MinMover MinMover.movemap MinMover.score_function

C++: protocols::simple_moves::MinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, : pyrosetta.rosetta.protocols.simple_moves.MinMover) → pyrosetta.rosetta.protocols.simple_moves.MinMover

C++: protocols::simple_moves::MinMover::operator=(const class protocols::simple_moves::MinMover &) –> class protocols::simple_moves::MinMover &

cartesian(*args, **kwargs)

Overloaded function.

1. cartesian(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, newval: bool) -> None

C++: protocols::simple_moves::MinMover::cartesian(bool) –> void

2. cartesian(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> bool

C++: protocols::simple_moves::MinMover::cartesian() const –> 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.simple_moves.MinMover) → pyrosetta.rosetta.protocols.moves.Mover

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

complex_type_generator_for_min_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::MinMover::complex_type_generator_for_min_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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>

deriv_check(*args, **kwargs)

Overloaded function.

1. deriv_check(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, deriv_check_in: bool) -> None

C++: protocols::simple_moves::MinMover::deriv_check(bool) –> void

2. deriv_check(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> bool

C++: protocols::simple_moves::MinMover::deriv_check() const –> bool

explicitly_set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) → pyrosetta.rosetta.core.kinematics.MoveMap

Get the explicitly set movemap object, if present, nullptr if not

Will not create a default or look at the MoveMapFactory

C++: protocols::simple_moves::MinMover::explicitly_set_movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

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

C++: protocols::simple_moves::MinMover::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.simple_moves.MinMover) → str

C++: protocols::simple_moves::MinMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(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

max_iter(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, max_iter_in: int) → None

C++: protocols::simple_moves::MinMover::max_iter(unsigned long) –> void

min_options(*args, **kwargs)

Overloaded function.

1. min_options(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> pyrosetta.rosetta.core.optimization.MinimizerOptions

allow non-const access to the internal minimizer options object

C++: protocols::simple_moves::MinMover::min_options() –> class std::shared_ptr<class core::optimization::MinimizerOptions>

2. min_options(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, min_options: pyrosetta.rosetta.core.optimization.MinimizerOptions) -> None

directly set the internal minimizer options object

C++: protocols::simple_moves::MinMover::min_options(class std::shared_ptr<class core::optimization::MinimizerOptions>) –> void

min_type(*args, **kwargs)

Overloaded function.

1. min_type(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, min_type_in: str) -> None

C++: protocols::simple_moves::MinMover::min_type(class std::basic_string<char>) –> void

2. min_type(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> str

C++: protocols::simple_moves::MinMover::min_type() const –> std::string

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

Sets the MoveMap to <movemap_in>

determines which DOF to minimize

example(s):

minmover.movemap(movemap1)

See also:

MinMover MinMover.apply MinMover.score_function MoveMap

C++: protocols::simple_moves::MinMover::movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> void

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for the pose

This is the preferred version to call.

C++: protocols::simple_moves::MinMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, mmf: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

Sets the MoveMapFactory

The MoveMapFactory will be used to construct a MoveMap if an explicit one isn’t set

C++: protocols::simple_moves::MinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::MinMover::mover_name() –> std::string

name() → str

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

nb_list(*args, **kwargs)

Overloaded function.

1. nb_list(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, nb_list_in: bool) -> None

core::optimization::MinimizerOptions::use_nblist(bool)

C++: protocols::simple_moves::MinMover::nb_list(bool) –> void

2. nb_list(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> bool

core::optimization::MinimizerOptions::use_nblist()

C++: protocols::simple_moves::MinMover::nb_list() const –> bool

omega(*args, **kwargs)

Overloaded function.

1. omega(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> bool

C++: protocols::simple_moves::MinMover::omega() const –> bool

2. omega(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, b: bool) -> None

C++: protocols::simple_moves::MinMover::omega(const bool) –> void

parse_dof_task_type(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, tag_name: str, dof_type: pyrosetta.rosetta.core.id.DOF_Type, torsion_type: pyrosetta.rosetta.core.id.TorsionType, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::simple_moves::MinMover::parse_dof_task_type(const class std::basic_string<char> &, enum core::id::DOF_Type, enum core::id::TorsionType, class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_dof_tasks(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::simple_moves::MinMover::parse_dof_tasks(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::simple_moves::MinMover::parse_movemap_factory(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::MinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

score_diff_after_minimization(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) → float

C++: protocols::simple_moves::MinMover::score_diff_after_minimization() const –> double

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <scorefxn_in>

determines which function to minimize

example(s):

minmover.score_function(scorefxn)

See also:

MinMover MinMover.apply MinMover.movemap ScoreFunction

C++: protocols::simple_moves::MinMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

2. score_function(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::MinMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_movemap(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::simple_moves::MinMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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.simple_moves.MinMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::MinMover::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

tolerance(*args, **kwargs)

Overloaded function.

1. tolerance(self: pyrosetta.rosetta.protocols.simple_moves.MinMover, tolerance_in: float) -> None

C++: protocols::simple_moves::MinMover::tolerance(double) –> void

2. tolerance(self: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> float

C++: protocols::simple_moves::MinMover::tolerance() const –> double

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.simple_moves.MinPackMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.

__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.simple_moves.MinPackMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, arg0: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) -> 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.simple_moves.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::MinPackMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, : pyrosetta.rosetta.protocols.simple_moves.MinPackMover) → pyrosetta.rosetta.protocols.simple_moves.MinPackMover

C++: protocols::simple_moves::MinPackMover::operator=(const class protocols::simple_moves::MinPackMover &) –> class protocols::simple_moves::MinPackMover &

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.simple_moves.MinPackMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::MinPackMover::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.simple_moves.MinPackMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::MinPackMover::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.simple_moves.MinPackMover) → str

C++: protocols::simple_moves::MinPackMover::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) → None

C++: protocols::simple_moves::MinPackMover::init() –> void

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

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

mover_name() → str

C++: protocols::simple_moves::MinPackMover::mover_name() –> std::string

name() → str

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

off_rotamer_pack(*args, **kwargs)

Overloaded function.

1. off_rotamer_pack(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, : bool) -> None

C++: protocols::simple_moves::MinPackMover::off_rotamer_pack(bool) –> void

2. off_rotamer_pack(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) -> bool

C++: protocols::simple_moves::MinPackMover::off_rotamer_pack() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::MinPackMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::MinPackMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

2. score_function(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::MinPackMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

task(*args, **kwargs)

Overloaded function.

1. task(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::simple_moves::MinPackMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

2. task(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::simple_moves::MinPackMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::MinPackMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::MinPackMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_is_valid(self: pyrosetta.rosetta.protocols.simple_moves.MinPackMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::MinPackMover::task_is_valid(const class core::pose::Pose &) const –> bool

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

Adds variant types to selected residues

__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.simple_moves.ModifyVariantTypeMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) -> 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.simple_moves.ModifyVariantTypeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ModifyVariantTypeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, : pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover

C++: protocols::simple_moves::ModifyVariantTypeMover::operator=(const class protocols::simple_moves::ModifyVariantTypeMover &) –> class protocols::simple_moves::ModifyVariantTypeMover &

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.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ModifyVariantTypeMover::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.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ModifyVariantTypeMover::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.simple_moves.ModifyVariantTypeMover) → str

C++: protocols::simple_moves::ModifyVariantTypeMover::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

mover_name() → str

C++: protocols::simple_moves::ModifyVariantTypeMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ModifyVariantTypeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

Get the ResidueSelector used by this mover.

C++: protocols::simple_moves::ModifyVariantTypeMover::residue_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

set_add_target_types(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, types_in: pyrosetta.rosetta.utility.vector1_std_string) → None

Set the types to add.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_add_target_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

set_additional_type_to_add(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, type_in: str) → None

Append a single type to the list to add.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_add(const class std::basic_string<char> &) –> void

set_additional_type_to_remove(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, type_in: str) → None

Append a single type to the list to remove.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_additional_type_to_remove(const class std::basic_string<char> &) –> 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_remove_target_types(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, types_in: pyrosetta.rosetta.utility.vector1_std_string) → None

Set the types to remove.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_remove_target_types(const class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the ResidueSelector used by this mover.

C++: protocols::simple_moves::ModifyVariantTypeMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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

set_update_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover, setting: bool) → None

Set whether polymer bond-dependent atoms should be updated after updating variant types.

Defaults to true. Set this to false to preserve polymer bond-dependent atom positions.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::set_update_polymer_bond_dependent_atoms(const bool) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(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

update_polymer_bond_dependent_atoms(self: pyrosetta.rosetta.protocols.simple_moves.ModifyVariantTypeMover) → bool

Get whether polymer bond-dependent atoms should be updated after updating variant types.

Vikram K. Mulligan (vmullig.edu).

C++: protocols::simple_moves::ModifyVariantTypeMover::update_polymer_bond_dependent_atoms() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.MutateResidue

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to mutate a single residue

__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.simple_moves.MutateResidue) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, arg0: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target: int, new_res: str) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target: int, new_res: int) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target: int, aa: pyrosetta.rosetta.core.chemical.AA) -> 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.simple_moves.MutateResidue, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::MutateResidue::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, : pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.simple_moves.MutateResidue

C++: protocols::simple_moves::MutateResidue::operator=(const class protocols::simple_moves::MutateResidue &) –> class protocols::simple_moves::MutateResidue &

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.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::MutateResidue::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.simple_moves.MutateResidue) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::MutateResidue::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.simple_moves.MutateResidue) → str

C++: protocols::simple_moves::MutateResidue::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

make_mutation(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, : pyrosetta.rosetta.core.pose.Pose, : int) → None

C++: protocols::simple_moves::MutateResidue::make_mutation(class core::pose::Pose &, unsigned long) –> void

mover_name() → str

C++: protocols::simple_moves::MutateResidue::mover_name() –> std::string

name() → str

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

preserve_atom_coords(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → bool

Get whether the mover should try to preserve atoms’ xyz coordinates or not.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::preserve_atom_coords() –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::MutateResidue::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → str

Get the residue to mutate to.

This is the full name, not the three-letter code.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::res_name() –> std::string

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_preserve_atom_coords(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, val: bool) → None

Set whether the mover should try to preserve atoms’ xyz coordinates or not.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_preserve_atom_coords(const bool) –> void

set_res_name(*args, **kwargs)

Overloaded function.

1. set_res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, name_in: str) -> None

Set the residue to mutate to.

This is the full name, not the three-letter code.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_res_name(const class std::basic_string<char> &) –> void

2. set_res_name(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::simple_moves::MutateResidue::set_res_name(const enum core::chemical::AA &) –> void

set_selector(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, selector_in: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set a selector if specified by the user

C++: protocols::simple_moves::MutateResidue::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_target(*args, **kwargs)

Overloaded function.

1. set_target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target_in: str) -> None

Set this mover’s target residue index.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_target(const class std::basic_string<char> &) –> void

2. set_target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, target_in: int) -> None

Set this mover’s target residue index, based on the Rosetta indexing.

C++: protocols::simple_moves::MutateResidue::set_target(const unsigned long) –> 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

set_update_polymer_dependent(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue, setting: bool) → None

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::set_update_polymer_dependent(const bool) –> void

show(*args, **kwargs)

Overloaded function.

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

Outputs details about the Mover, including current settings.

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

target(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → str

Get this mover’s target residue index.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::target() const –> std::string

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

update_polymer_dependent(self: pyrosetta.rosetta.protocols.simple_moves.MutateResidue) → bool

Set whether this mover updates polymer-dependent atoms in the residue that it mutates.

Vikram K. Mulligan (vmullig.edu)

C++: protocols::simple_moves::MutateResidue::update_polymer_dependent() const –> bool

class pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing

Common Methods:

PackRotamersMover.apply

please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!

__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.simple_moves.PackRotamersMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, : str) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, arg0: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

doc

5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, arg0: pyrosetta.rosetta.core.scoring.ScoreFunction, arg1: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

doc

6. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, nloop: int) -> None
7. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, arg0: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → str

__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.simple_moves.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Performs side-chain packing based on the input PackerTask

using the input ScoreFunction

example(s):

packmover.apply(pose)

See Also:

PackerTask ScoreFunction

C++: protocols::simple_moves::PackRotamersMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, : pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover

C++: protocols::simple_moves::PackRotamersMover::operator=(const class protocols::simple_moves::PackRotamersMover &) –> class protocols::simple_moves::PackRotamersMover &

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.simple_moves.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

complex_type_generator_for_pack_rotamers_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.simple_moves.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PackRotamersMover::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.simple_moves.PackRotamersMover) → str

C++: protocols::simple_moves::PackRotamersMover::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

ig(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: protocols::simple_moves::PackRotamersMover::ig() const –> class std::shared_ptr<const class core::pack::interaction_graph::AnnealableGraphBase>

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

mover_name() → str

C++: protocols::simple_moves::PackRotamersMover::mover_name() –> std::string

name() → str

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

nloop(*args, **kwargs)

Overloaded function.

1. nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, nloop_in: int) -> None

C++: protocols::simple_moves::PackRotamersMover::nloop(unsigned long) –> void

2. nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> int

C++: protocols::simple_moves::PackRotamersMover::nloop() const –> unsigned long

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::PackRotamersMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

rotamer_sets(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: protocols::simple_moves::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

2. score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

task(*args, **kwargs)

Overloaded function.

1. task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

2. task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_is_valid(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Bases: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover

a mover that packs the side-chains using a rotamer library in a lazy fashion.

__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.simple_moves.PackRotamersMoverLazy, arg0: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, arg0: pyrosetta.rosetta.core.scoring.ScoreFunction, arg1: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, nloop: int) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, arg0: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → str

__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.simple_moves.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Performs side-chain packing based on the input PackerTask

using the input ScoreFunction

example(s):

packmover.apply(pose)

See Also:

PackerTask ScoreFunction

C++: protocols::simple_moves::PackRotamersMover::apply(class core::pose::Pose &) –> void

apply_to_rotpack(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → None

C++: protocols::simple_moves::PackRotamersMoverLazy::apply_to_rotpack(class core::pose::Pose &, class utility::vector0<int, class std::allocator<int> >) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, : pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy) → pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy

C++: protocols::simple_moves::PackRotamersMoverLazy::operator=(const class protocols::simple_moves::PackRotamersMoverLazy &) –> class protocols::simple_moves::PackRotamersMoverLazy &

call_setup(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMoverLazy, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::PackRotamersMoverLazy::call_setup(class core::pose::Pose &) –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

complex_type_generator_for_pack_rotamers_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.simple_moves.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PackRotamersMover::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.simple_moves.PackRotamersMover) → str

C++: protocols::simple_moves::PackRotamersMover::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

ig(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

C++: protocols::simple_moves::PackRotamersMover::ig() const –> class std::shared_ptr<const class core::pack::interaction_graph::AnnealableGraphBase>

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

mover_name() → str

C++: protocols::simple_moves::PackRotamersMover::mover_name() –> std::string

name() → str

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

nloop(*args, **kwargs)

Overloaded function.

1. nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, nloop_in: int) -> None

C++: protocols::simple_moves::PackRotamersMover::nloop(unsigned long) –> void

2. nloop(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> int

C++: protocols::simple_moves::PackRotamersMover::nloop() const –> unsigned long

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::PackRotamersMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

rotamer_sets(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: protocols::simple_moves::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

2. score_function(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

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

task(*args, **kwargs)

Overloaded function.

1. task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

2. task(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::simple_moves::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::simple_moves::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_is_valid(self: pyrosetta.rosetta.protocols.simple_moves.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

Random perturbation, followed by minimization

__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.simple_moves.PertMinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) → str

__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.simple_moves.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::PertMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, : pyrosetta.rosetta.protocols.simple_moves.PertMinMover) → pyrosetta.rosetta.protocols.simple_moves.PertMinMover

C++: protocols::simple_moves::PertMinMover::operator=(const class protocols::simple_moves::PertMinMover &) –> class protocols::simple_moves::PertMinMover &

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.simple_moves.PertMinMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PertMinMover::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.simple_moves.PertMinMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::PertMinMover::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.simple_moves.PertMinMover) → str

C++: protocols::simple_moves::PertMinMover::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

min(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::PertMinMover::min(class core::pose::Pose &) const –> void

movemap(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) → pyrosetta.rosetta.core.select.movemap.MoveMapFactory

C++: protocols::simple_moves::PertMinMover::movemap() const –> class std::shared_ptr<const class core::select::movemap::MoveMapFactory>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::PertMinMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::PertMinMover::mover_name() –> std::string

name() → str

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

pert(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, pose: pyrosetta.rosetta.core.pose.Pose, resi: pyrosetta.rosetta.utility.vector1_bool) → None

C++: protocols::simple_moves::PertMinMover::pert(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

pert_size(*args, **kwargs)

Overloaded function.

1. pert_size(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> float

C++: protocols::simple_moves::PertMinMover::pert_size() const –> double

2. pert_size(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: float) -> None

C++: protocols::simple_moves::PertMinMover::pert_size(double) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::PertMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

residues(*args, **kwargs)

Overloaded function.

1. residues(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::simple_moves::PertMinMover::residues() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. residues(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::PertMinMover::residues(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

sc_only(*args, **kwargs)

Overloaded function.

1. sc_only(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> bool

C++: protocols::simple_moves::PertMinMover::sc_only() const –> bool

2. sc_only(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: bool) -> None

C++: protocols::simple_moves::PertMinMover::sc_only(bool) –> void

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::PertMinMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

2. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::PertMinMover::scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.simple_moves.PertMinMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::PertMinMover::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

uniform(*args, **kwargs)

Overloaded function.

1. uniform(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover) -> bool

C++: protocols::simple_moves::PertMinMover::uniform() const –> bool

2. uniform(self: pyrosetta.rosetta.protocols.simple_moves.PertMinMover, setting: bool) -> None

C++: protocols::simple_moves::PertMinMover::uniform(bool) –> void

class pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Simple class that flips a random omega selected from a movemap 180 degrees

__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.simple_moves.RandomOmegaFlipMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, move_map: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) -> 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.simple_moves.RandomOmegaFlipMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::RandomOmegaFlipMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, : pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover

C++: protocols::simple_moves::RandomOmegaFlipMover::operator=(const class protocols::simple_moves::RandomOmegaFlipMover &) –> class protocols::simple_moves::RandomOmegaFlipMover &

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.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::RandomOmegaFlipMover::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.simple_moves.RandomOmegaFlipMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::RandomOmegaFlipMover::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.simple_moves.RandomOmegaFlipMover) → str

C++: protocols::simple_moves::RandomOmegaFlipMover::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

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RandomOmegaFlipMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::RandomOmegaFlipMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::RandomOmegaFlipMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::RandomOmegaFlipMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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.simple_moves.RandomTorsionMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Simple class that randomly purturbs a random torsion selected from a movemap

__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.simple_moves.RandomTorsionMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory, max_angle: float, num_moves: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, move_map: pyrosetta.rosetta.core.kinematics.MoveMap, max_angle: float, num_moves: int) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) -> 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.simple_moves.RandomTorsionMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::RandomTorsionMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, : pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover

C++: protocols::simple_moves::RandomTorsionMover::operator=(const class protocols::simple_moves::RandomTorsionMover &) –> class protocols::simple_moves::RandomTorsionMover &

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.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::RandomTorsionMover::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.simple_moves.RandomTorsionMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::RandomTorsionMover::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.simple_moves.RandomTorsionMover) → str

C++: protocols::simple_moves::RandomTorsionMover::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

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RandomTorsionMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::RandomTorsionMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::RandomTorsionMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::RandomTorsionMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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.simple_moves.RepackSidechainsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A protocols::moves::Mover that packs the side-chains (very similar to pack_missing_sidechains()

__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.simple_moves.RepackSidechainsMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover) -> 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.simple_moves.RepackSidechainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::RepackSidechainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover, : pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover) → pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover

C++: protocols::simple_moves::RepackSidechainsMover::operator=(const class protocols::simple_moves::RepackSidechainsMover &) –> class protocols::simple_moves::RepackSidechainsMover &

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.simple_moves.RepackSidechainsMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::RepackSidechainsMover::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.simple_moves.RepackSidechainsMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::simple_moves::RepackSidechainsMover::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.simple_moves.RepackSidechainsMover) → str

C++: protocols::simple_moves::RepackSidechainsMover::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

scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::RepackSidechainsMover::scorefxn() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.RepackSidechainsMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::simple_moves::RepackSidechainsMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> 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.simple_moves.ReportEffectivePKA

Bases: pyrosetta.rosetta.protocols.moves.Mover

scale density map intensities to match a pose’s

__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.simple_moves.ReportEffectivePKA) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, arg0: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) -> 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.simple_moves.ReportEffectivePKA, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ReportEffectivePKA::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, : pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA

C++: protocols::simple_moves::ReportEffectivePKA::operator=(const class protocols::simple_moves::ReportEffectivePKA &) –> class protocols::simple_moves::ReportEffectivePKA &

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.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ReportEffectivePKA::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.simple_moves.ReportEffectivePKA) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ReportEffectivePKA::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.simple_moves.ReportEffectivePKA) → str

C++: protocols::simple_moves::ReportEffectivePKA::get_name() const –> std::string

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

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

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

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

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

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

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

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

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

non-const accessor

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

init(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) → None

C++: protocols::simple_moves::ReportEffectivePKA::init() –> void

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

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

mover_name() → str

C++: protocols::simple_moves::ReportEffectivePKA::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ReportEffectivePKA::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::ReportEffectivePKA::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.ReportEffectivePKA) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::ReportEffectivePKA::task_factory() const –> class std::shared_ptr<class core::pack::task::TaskFactory>

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.simple_moves.RepulsiveOnlyMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

this mover replace designated residues with glycines, and then assigns a “REPLONLY” residue type to those glycines. Those “REPLONLY” residues will make only repulsive contributions to the overall energy.

__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.simple_moves.RepulsiveOnlyMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover) -> 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.simple_moves.RepulsiveOnlyMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::RepulsiveOnlyMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, : pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover) → pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover

C++: protocols::simple_moves::RepulsiveOnlyMover::operator=(const class protocols::simple_moves::RepulsiveOnlyMover &) –> class protocols::simple_moves::RepulsiveOnlyMover &

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.simple_moves.RepulsiveOnlyMover) → str

C++: protocols::simple_moves::RepulsiveOnlyMover::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_mutate_to_glycine(self: pyrosetta.rosetta.protocols.simple_moves.RepulsiveOnlyMover, setting: bool) → None

C++: protocols::simple_moves::RepulsiveOnlyMover::set_mutate_to_glycine(bool) –> 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.simple_moves.ReturnSidechainMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This class takes two poses, one at instantiation and one at apply. It copies the residue type set and chi information from its kept pose to the apply pose. The intended purpose is for “returning” known sidechains to a pose that was temporarily in centroid mode, although it may work with other residue type sets.

__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.simple_moves.ReturnSidechainMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: int) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, pose_in: pyrosetta.rosetta.core.pose.Pose, start_res: int, end_res: int) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.utility.vector1_bool) -> None

doc

6. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: pyrosetta.rosetta.utility.vector1_bool, arg2: int) -> None

doc

7. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, pose_in: pyrosetta.rosetta.core.pose.Pose, allow_chi_in: pyrosetta.rosetta.utility.vector1_bool, start_res: int, end_res: int) -> None
8. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → str

__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.simple_moves.ReturnSidechainMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ReturnSidechainMover::apply(class core::pose::Pose &) –> void

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

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

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.simple_moves.ReturnSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ReturnSidechainMover::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.simple_moves.ReturnSidechainMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ReturnSidechainMover::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_end_res(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → int

C++: protocols::simple_moves::ReturnSidechainMover::get_end_res() const –> unsigned long

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.simple_moves.ReturnSidechainMover) → str

C++: protocols::simple_moves::ReturnSidechainMover::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_start_res(self: pyrosetta.rosetta.protocols.simple_moves.ReturnSidechainMover) → int

C++: protocols::simple_moves::ReturnSidechainMover::get_start_res() const –> unsigned long

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

C++: protocols::simple_moves::ReturnSidechainMover::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.simple_moves.RingConformationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Based on a given MoveMap, this mover selects movable cyclic residues and flips their rings to an idealized ring conformer.

__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.simple_moves.RingConformationMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, input_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → str

__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.simple_moves.RingConformationMover, input_pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply the corresponding move to <input_pose>.

C++: protocols::simple_moves::RingConformationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, object_to_copy: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.simple_moves.RingConformationMover

C++: protocols::simple_moves::RingConformationMover::operator=(const class protocols::simple_moves::RingConformationMover &) –> class protocols::simple_moves::RingConformationMover &

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.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.moves.Mover

Return the name of the Mover.

C++: protocols::simple_moves::RingConformationMover::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.simple_moves.RingConformationMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::RingConformationMover::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.simple_moves.RingConformationMover) → str

C++: protocols::simple_moves::RingConformationMover::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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the current MoveMap.

C++: protocols::simple_moves::RingConformationMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

Set the MoveMap.

C++: protocols::simple_moves::RingConformationMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

Set the MoveMapFactory.

C++: protocols::simple_moves::RingConformationMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::RingConformationMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::RingConformationMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None

Register options with the option system.

C++: protocols::simple_moves::RingConformationMover::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

sample_all_conformers(*args, **kwargs)

Overloaded function.

1. sample_all_conformers(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover) -> bool

Get whether or not this Mover will sample all ring conformers, regardless of energy.

C++: protocols::simple_moves::RingConformationMover::sample_all_conformers() const –> bool

2. sample_all_conformers(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, setting: bool) -> None

Set whether or not this Mover will sample all ring conformers, regardless of energy.

C++: protocols::simple_moves::RingConformationMover::sample_all_conformers(bool) –> 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.simple_moves.RingConformationMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMover, output: pyrosetta.rosetta.std.ostream) -> None

Generate string representation of RingConformationMover for debugging purposes.

C++: protocols::simple_moves::RingConformationMover::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.simple_moves.RingConformationMoverCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

MoverCreator allowing the MoverFactory to create a RingConformationMover

__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.simple_moves.RingConformationMoverCreator) → 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.simple_moves.RingConformationMoverCreator, : pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator

C++: protocols::simple_moves::RingConformationMoverCreator::operator=(const class protocols::simple_moves::RingConformationMoverCreator &) –> class protocols::simple_moves::RingConformationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover

Static method that returns the keyname for performance reasons.

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

keyname(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator) → str

C++: protocols::simple_moves::RingConformationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.simple_moves.RingConformationMoverCreator, xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set.

__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.simple_moves.RotamerizeMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, arg0: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover) -> 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.simple_moves.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::RotamerizeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, : pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover) → pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover

C++: protocols::simple_moves::RotamerizeMover::operator=(const class protocols::simple_moves::RotamerizeMover &) –> class protocols::simple_moves::RotamerizeMover &

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.simple_moves.RotamerizeMover) → str

C++: protocols::simple_moves::RotamerizeMover::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

rotamer_sets(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: protocols::simple_moves::RotamerizeMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

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

task(*args, **kwargs)

Overloaded function.

1. task(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

C++: protocols::simple_moves::RotamerizeMover::task(class std::shared_ptr<class core::pack::task::PackerTask>) –> void

2. task(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

C++: protocols::simple_moves::RotamerizeMover::task() const –> class std::shared_ptr<class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::simple_moves::RotamerizeMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

C++: protocols::simple_moves::RotamerizeMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_is_valid(self: pyrosetta.rosetta.protocols.simple_moves.RotamerizeMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::RotamerizeMover::task_is_valid(const class core::pose::Pose &) const –> bool

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

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

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Bases: pyrosetta.rosetta.protocols.moves.Mover

performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. Unlike the classic MinMover, the only method for setting Minimization options is via the MinimizerOptions class.

__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.simple_moves.SaneMinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover, name: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover, arg0: pyrosetta.rosetta.core.kinematics.MoveMap, arg1: pyrosetta.rosetta.core.scoring.ScoreFunction, arg2: pyrosetta.rosetta.core.optimization.MinimizerOptions) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction, min_options_in: pyrosetta.rosetta.core.optimization.MinimizerOptions, cartesian: bool) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) -> 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.simple_moves.SaneMinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Minimizes the DOFs of pose specified in the MoveMap

C++: protocols::simple_moves::SaneMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover, : pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) → pyrosetta.rosetta.protocols.simple_moves.SaneMinMover

C++: protocols::simple_moves::SaneMinMover::operator=(const class protocols::simple_moves::SaneMinMover &) –> class protocols::simple_moves::SaneMinMover &

cartesian(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) → bool

C++: protocols::simple_moves::SaneMinMover::cartesian() const –> 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.simple_moves.SaneMinMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SaneMinMover::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.simple_moves.SaneMinMover) → str

C++: protocols::simple_moves::SaneMinMover::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

min_options(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) → pyrosetta.rosetta.core.optimization.MinimizerOptions

C++: protocols::simple_moves::SaneMinMover::min_options() const –> class std::shared_ptr<class core::optimization::MinimizerOptions>

move_map(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::SaneMinMover::move_map() const –> class std::shared_ptr<class core::kinematics::MoveMap>

mover_name() → str

C++: protocols::simple_moves::SaneMinMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SaneMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

score_function(self: pyrosetta.rosetta.protocols.simple_moves.SaneMinMover) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::simple_moves::SaneMinMover::score_function() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

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.simple_moves.SetTorsion

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to change one torsion angle

__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.simple_moves.SetTorsion) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, arg0: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) -> 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).

add_perturbation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, mag_in: float) → None

Add a perturbation magnitude to the list of perturbation magnitudes.

Checks for non-negative magnitude. After this operation, the perturbation_magnitude_ vector is one entry longer.

C++: protocols::simple_moves::SetTorsion::add_perturbation_magnitude(const double &) –> void

add_perturbation_type(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, type_in: str) → None

Add a perturbation type to the list of perturbation types.

Currently only allows “uniform” or “gaussian”. Checks for proper input. After this operation, the perturbation_type_ vector is one entry longer.

C++: protocols::simple_moves::SetTorsion::add_perturbation_type(const class std::basic_string<char> &) –> void

angle(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int, old_angle: float) → float

Actually get the value that the torsion will be set to.

Depending on settings, this will look up a value, generate a random value, or perturb an input value.

C++: protocols::simple_moves::SetTorsion::angle(const unsigned long, const double &) const –> double

apply(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SetTorsion::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, : pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.simple_moves.SetTorsion

C++: protocols::simple_moves::SetTorsion::operator=(const class protocols::simple_moves::SetTorsion &) –> class protocols::simple_moves::SetTorsion &

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.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SetTorsion::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.simple_moves.SetTorsion) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SetTorsion::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_fold_tree_root(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → int

Returns the residue index that will serve as the root of the FoldTree for the SetTorsion operation.

C++: protocols::simple_moves::SetTorsion::get_fold_tree_root() const –> unsigned long

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.simple_moves.SetTorsion) → str

C++: protocols::simple_moves::SetTorsion::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

mover_name() → str

C++: protocols::simple_moves::SetTorsion::mover_name() –> std::string

n_torsion_sets(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion) → int

C++: protocols::simple_moves::SetTorsion::n_torsion_sets() const –> unsigned long

name() → str

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

perturbation_magnitude(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, index: int) → float

Get a perturbation magnitude.

C++: protocols::simple_moves::SetTorsion::perturbation_magnitude(const unsigned long) const –> double

perturbation_type(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, index: int) → pyrosetta.rosetta.protocols.simple_moves.TorsionPerturbType

Get a perturbation type.

C++: protocols::simple_moves::SetTorsion::perturbation_type(const unsigned long) const –> enum protocols::simple_moves::TorsionPerturbType

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SetTorsion::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

residue_list(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::SetTorsion::residue_list(unsigned long, const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

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_fold_tree_root(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, root: int) → None

Sets a residue index that will serve as the root of the FoldTree for the SetTorsion operation.

The FoldTree is reset afterwards (i.e. the mover does not permanently change the FoldTree).

C++: protocols::simple_moves::SetTorsion::set_fold_tree_root(const unsigned long) –> 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

torsion_ct_name(: str) → str

C++: protocols::simple_moves::SetTorsion::torsion_ct_name(class std::basic_string<char>) –> std::string

torsion_name(self: pyrosetta.rosetta.protocols.simple_moves.SetTorsion, iset: int) → str

C++: protocols::simple_moves::SetTorsion::torsion_name(const unsigned long) –> std::string

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.simple_moves.SetupMetalsMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A protocols::moves::Mover that

__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.simple_moves.SetupMetalsMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str

__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.simple_moves.SetupMetalsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SetupMetalsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover

C++: protocols::simple_moves::SetupMetalsMover::operator=(const class protocols::simple_moves::SetupMetalsMover &) –> class protocols::simple_moves::SetupMetalsMover &

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.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SetupMetalsMover::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.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.protocols.moves.Mover

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

get_add_constraints(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool

C++: protocols::simple_moves::SetupMetalsMover::get_add_constraints() const –> bool

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_constraints_only(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool

C++: protocols::simple_moves::SetupMetalsMover::get_constraints_only() const –> bool

get_contact_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str

C++: protocols::simple_moves::SetupMetalsMover::get_contact_resnums_string() const –> std::string

get_contact_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::simple_moves::SetupMetalsMover::get_contact_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

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_metal_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str

C++: protocols::simple_moves::SetupMetalsMover::get_metal_resnums_string() const –> std::string

get_metal_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

C++: protocols::simple_moves::SetupMetalsMover::get_metal_selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

get_metals_angle_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float

C++: protocols::simple_moves::SetupMetalsMover::get_metals_angle_constraint_multiplier() const –> double

get_metals_detection_LJ_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float

C++: protocols::simple_moves::SetupMetalsMover::get_metals_detection_LJ_multiplier() const –> double

get_metals_distance_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → float

C++: protocols::simple_moves::SetupMetalsMover::get_metals_distance_constraint_multiplier() const –> double

get_name(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → str

C++: protocols::simple_moves::SetupMetalsMover::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_remove_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover) → bool

C++: protocols::simple_moves::SetupMetalsMover::get_remove_hydrogens() const –> bool

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

mover_name() → str

C++: protocols::simple_moves::SetupMetalsMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SetupMetalsMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_add_constraints(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None

C++: protocols::simple_moves::SetupMetalsMover::set_add_constraints(bool) –> void

set_constraints_only(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None

C++: protocols::simple_moves::SetupMetalsMover::set_constraints_only(bool) –> void

set_contact_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : str) → None

C++: protocols::simple_moves::SetupMetalsMover::set_contact_resnums_string(class std::basic_string<char>) –> void

set_contact_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::simple_moves::SetupMetalsMover::set_contact_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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_metal_resnums_string(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : str) → None

C++: protocols::simple_moves::SetupMetalsMover::set_metal_resnums_string(class std::basic_string<char>) –> void

set_metal_selector(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

C++: protocols::simple_moves::SetupMetalsMover::set_metal_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_metals_angle_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None

C++: protocols::simple_moves::SetupMetalsMover::set_metals_angle_constraint_multiplier(double) –> void

set_metals_detection_LJ_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None

C++: protocols::simple_moves::SetupMetalsMover::set_metals_detection_LJ_multiplier(double) –> void

set_metals_distance_constraint_multiplier(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : float) → None

C++: protocols::simple_moves::SetupMetalsMover::set_metals_distance_constraint_multiplier(double) –> 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_remove_hydrogens(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, : bool) → None

C++: protocols::simple_moves::SetupMetalsMover::set_remove_hydrogens(bool) –> 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.simple_moves.SetupMetalsMover) -> None
2. show(self: pyrosetta.rosetta.protocols.simple_moves.SetupMetalsMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::simple_moves::SetupMetalsMover::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.simple_moves.ShearMover

Bases: pyrosetta.rosetta.protocols.simple_moves.BackboneMover

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a ‘shearing’ effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods:

ShearMover.apply

__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.simple_moves.ShearMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap, temperature_in: float, nmoves_in: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, arg0: pyrosetta.rosetta.protocols.simple_moves.ShearMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → str

__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).

angle_max(*args, **kwargs)

Overloaded function.

1. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Sets the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

2. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(‘H’, 25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

3. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures

‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None

virtual functions that get overridden or called from the inheriting classes

C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, : pyrosetta.rosetta.protocols.simple_moves.ShearMover) → pyrosetta.rosetta.protocols.simple_moves.ShearMover

C++: protocols::simple_moves::ShearMover::operator=(const class protocols::simple_moves::ShearMover &) –> class protocols::simple_moves::ShearMover &

backbone_mover_complex_type_namer(tag_name: str) → str

C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(class std::basic_string<char>) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None

C++: protocols::simple_moves::BackboneMover::clear() –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover) → pyrosetta.rosetta.protocols.moves.Mover

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

complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

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

C++: protocols::simple_moves::ShearMover::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_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:

bbmover.angle_max(‘H’)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

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.simple_moves.ShearMover) → str

C++: protocols::simple_moves::ShearMover::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 > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::ShearMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::ShearMover::mover_name() –> std::string

name() → str

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

new_omega(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_omega() –> double

new_phi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_phi() –> double

new_psi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_psi() –> double

nmoves(*args, **kwargs)

Overloaded function.

1. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

2. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::ShearMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

if set, this scorefunction will be used instead of the original rama method (default = not set)

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

2. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)

Overloaded function.

1. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns the residue selector which can be used to dynamically select residues to perturb

at runtime

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, angle_in: float) → None

C++: protocols::simple_moves::ShearMover::set_angles(double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ShearMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)

Overloaded function.

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

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

temperature(*args, **kwargs)

Overloaded function.

1. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

Properties set/get functions

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

2. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::ShearMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.ShearMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::simple_moves::ShearMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

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.simple_moves.SimpleThreadingMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover functions to thread the sequence of a region onto the given pose. Nothing fancy here. For more fancy things see protocols/comparative_modeling.

It does the threading by allowing the task to only enable these residues and then does a repacking. Optionally repack neighbors so we save one more step. A sequence is just a string, additional ‘-‘ charactors denote to skip this position in the thread. Default is 5 rounds of packing.

__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.simple_moves.SimpleThreadingMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, thread_sequence: str, start_position: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) -> 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.simple_moves.SimpleThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SimpleThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, : pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover

C++: protocols::simple_moves::SimpleThreadingMover::operator=(const class protocols::simple_moves::SimpleThreadingMover &) –> class protocols::simple_moves::SimpleThreadingMover &

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.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SimpleThreadingMover::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.simple_moves.SimpleThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SimpleThreadingMover::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.simple_moves.SimpleThreadingMover) → str

C++: protocols::simple_moves::SimpleThreadingMover::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_neighbor_distance(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → float

C++: protocols::simple_moves::SimpleThreadingMover::get_neighbor_distance() const –> double

get_pack_neighbors(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover) → bool

C++: protocols::simple_moves::SimpleThreadingMover::get_pack_neighbors() const –> bool

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

mover_name() → str

C++: protocols::simple_moves::SimpleThreadingMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SimpleThreadingMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_neighbor_distance(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, neighbor_dis: float) → None

Set the packing distance for neighbor pack.

C++: protocols::simple_moves::SimpleThreadingMover::set_neighbor_distance(double) –> void

set_pack_neighbors(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, pack_neighbors: bool) → None

Pack the neighbor residues?

C++: protocols::simple_moves::SimpleThreadingMover::set_pack_neighbors(bool) –> void

set_pack_rounds(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, pack_rounds: int) → None

Set the number of pack rounds.

C++: protocols::simple_moves::SimpleThreadingMover::set_pack_rounds(unsigned long) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

Set the scorefunction used for packing.

C++: protocols::simple_moves::SimpleThreadingMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

set_sequence(self: pyrosetta.rosetta.protocols.simple_moves.SimpleThreadingMover, thread_sequence: str, start_position: int) → None

Set the sequence to thread onto the structure used in apply and where to start.

Can have ‘-‘ charactors in sequence to denote a gap in the threaded sequence.

C++: protocols::simple_moves::SimpleThreadingMover::set_sequence(class std::basic_string<char>, unsigned long) –> 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.simple_moves.SmallMover

Bases: pyrosetta.rosetta.protocols.simple_moves.BackboneMover

A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and the final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods:

SmallMover.apply SmallMover.angle_max

__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.simple_moves.SmallMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, movemap_in: pyrosetta.rosetta.core.kinematics.MoveMap, temperature_in: float, nmoves_in: int) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SmallMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → str

__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).

angle_max(*args, **kwargs)

Overloaded function.

1. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle: float) -> None

Sets the maximum angle of perturbation, independent of

secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const double) –> void

2. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str, angle: float) -> None

Sets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.) new_angle = old_angle +/- ( angle_max/2 )

Example:

bbmover.angle_max(‘H’, 25)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::angle_max(const char, const double) –> void

3. angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, angle_max_in: pyrosetta.rosetta.std.map_char_double) -> None

Sets the max angle of perturbation, for secondary structures

‘H’, ‘E’, and ‘L’. new_angle = old_angle +/- ( angle_max/2 )

C++: protocols::simple_moves::BackboneMover::angle_max(class std::map<char, double, struct std::less<char>, class std::allocator<struct std::pair<const char, double> > >) –> void

apply(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, : pyrosetta.rosetta.core.pose.Pose) → None

virtual functions that get overridden or called from the inheriting classes

C++: protocols::simple_moves::BackboneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, : pyrosetta.rosetta.protocols.simple_moves.SmallMover) → pyrosetta.rosetta.protocols.simple_moves.SmallMover

C++: protocols::simple_moves::SmallMover::operator=(const class protocols::simple_moves::SmallMover &) –> class protocols::simple_moves::SmallMover &

backbone_mover_complex_type_namer(tag_name: str) → str

C++: protocols::simple_moves::BackboneMover::backbone_mover_complex_type_namer(class std::basic_string<char>) –> std::string

check_rama(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

C++: protocols::simple_moves::BackboneMover::check_rama() –> bool

clear(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → None

C++: protocols::simple_moves::BackboneMover::clear() –> void

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover) → pyrosetta.rosetta.protocols.moves.Mover

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

complex_type_generator_for_backbone_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::simple_moves::BackboneMover::complex_type_generator_for_backbone_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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>

finalize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after all Monte Carlo trials are completed.

C++: protocols::canonical_sampling::ThermodynamicMover::finalize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

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

C++: protocols::simple_moves::SmallMover::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_angle_max(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, type: str) → float

Gets the max angle of perturbation for residues with <type>

secondary structure. (<type> must be ‘H’, ‘E’, or ‘L’.)

Example:

bbmover.angle_max(‘H’)

See also:

ShearMover SmallMover

C++: protocols::simple_moves::BackboneMover::get_angle_max(const char) const –> double

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.simple_moves.SmallMover) → str

C++: protocols::simple_moves::SmallMover::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 > > &

initialize_simulation(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, pose: pyrosetta.rosetta.core.pose.Pose, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover, cycle: int) → None

Callback executed before any Monte Carlo trials are attempted.

C++: protocols::canonical_sampling::ThermodynamicMover::initialize_simulation(class core::pose::Pose &, const class protocols::canonical_sampling::MetropolisHastingsMover &, unsigned long) –> void

is_multi_trial(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → bool

Return true if the move performs multiple trials on each apply.

last_inner_score_delta_over_temperature()

metropolis_hastings_mover()

set_metropolis_hastings_mover()

C++: protocols::canonical_sampling::ThermodynamicMover::is_multi_trial() –> bool

last_inner_score_delta_over_temperature(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

If this is a multi-trial move, return the change in internal

score/temperature caused by the last call to apply().

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::last_inner_score_delta_over_temperature() –> double

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → float

Return the proposal density ratio for last apply method.

C++: protocols::canonical_sampling::ThermodynamicMover::last_proposal_density_ratio() –> double

make_move(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::SmallMover::make_move(class core::pose::Pose &) –> bool

metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover) → pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t

If this is a multi-trial move, return the MetropolisHastingsMover

being used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::metropolis_hastings_mover() –> class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None

C++: protocols::simple_moves::BackboneMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

Get the movemap for this pose

C++: protocols::simple_moves::BackboneMover::movemap(const class core::pose::Pose &) –> class std::shared_ptr<const class core::kinematics::MoveMap>

movemap_factory(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

C++: protocols::simple_moves::BackboneMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void

mover_name() → str

C++: protocols::simple_moves::SmallMover::mover_name() –> std::string

name() → str

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

new_omega(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_omega() –> double

new_phi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_phi() –> double

new_psi(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → float

C++: protocols::simple_moves::BackboneMover::new_psi() –> double

nmoves(*args, **kwargs)

Overloaded function.

1. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, nmoves_in: int) -> None

C++: protocols::simple_moves::BackboneMover::nmoves(const unsigned long) –> void

2. nmoves(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> int

C++: protocols::simple_moves::BackboneMover::nmoves() const –> unsigned long

observe_after_metropolis(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: protocols::canonical_sampling::MetropolisHastingsMover) → None

Callback executed after the Metropolis criterion is evaluated.

C++: protocols::canonical_sampling::ThermodynamicMover::observe_after_metropolis(const class protocols::canonical_sampling::MetropolisHastingsMover &) –> void

preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) → bool

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::preserve_detailed_balance() const –> bool

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SmallMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

scorefxn(*args, **kwargs)

Overloaded function.

1. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

if set, this scorefunction will be used instead of the original rama method (default = not set)

C++: protocols::simple_moves::BackboneMover::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

2. scorefxn(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::simple_moves::BackboneMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

selector(*args, **kwargs)

Overloaded function.

1. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector

returns the residue selector which can be used to dynamically select residues to perturb

at runtime

C++: protocols::simple_moves::BackboneMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>

2. selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None

C++: protocols::simple_moves::BackboneMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void

set_angles(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, angle_in: float) → None

C++: protocols::simple_moves::SmallMover::set_angles(double) –> 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_metropolis_hastings_mover(self: pyrosetta.rosetta.protocols.canonical_sampling.ThermodynamicMover, metropolis_hastings_mover: pyrosetta.rosetta.std.weak_ptr_protocols_canonical_sampling_MetropolisHastingsMover_t) → None

If this is a multi-trial move, set the MetropolisHastingsMover to

be used internally.

is_multi_trial()

C++: protocols::canonical_sampling::ThermodynamicMover::set_metropolis_hastings_mover(class std::weak_ptr<class protocols::canonical_sampling::MetropolisHastingsMover>) –> 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_preserve_detailed_balance(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, preserve_detailed_balance: bool) → None

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

C++: protocols::simple_moves::BackboneMover::set_preserve_detailed_balance(bool) –> void

set_residue_selector(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) → None

Set the ResidueSelector that this mover will use.

Clones the input.

C++: protocols::simple_moves::BackboneMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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

setup_list(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SmallMover::setup_list(class core::pose::Pose &) –> void

show(*args, **kwargs)

Overloaded function.

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

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

temperature(*args, **kwargs)

Overloaded function.

1. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover, temperature_in: float) -> None

Properties set/get functions

C++: protocols::simple_moves::BackboneMover::temperature(const double) –> void

2. temperature(self: pyrosetta.rosetta.protocols.simple_moves.BackboneMover) -> float

C++: protocols::simple_moves::BackboneMover::temperature() const –> double

test_move(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SmallMover::test_move(class core::pose::Pose &) –> void

torsion_id_ranges(self: pyrosetta.rosetta.protocols.simple_moves.SmallMover, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_core_id_TorsionID_Range

get the TorsionIDs perturbed by the mover during moves, along with their ranges

C++: protocols::simple_moves::SmallMover::torsion_id_ranges(class core::pose::Pose &) –> class utility::vector1<class core::id::TorsionID_Range, class std::allocator<class core::id::TorsionID_Range> >

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.simple_moves.SmoothSymmetricFragmentMover

Bases: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover

A SymmetricFragmentMover that applies uniform sampling of fragments

__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.simple_moves.SmoothSymmetricFragmentMover, fragset: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, cost: pyrosetta.rosetta.protocols.simple_moves.FragmentCost, symmetric_residue: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str

__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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
2. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:

mover_3mer.apply(pose)

See also:

ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::SymmetricFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover

C++: protocols::simple_moves::SmoothSymmetricFragmentMover::operator=(const class protocols::simple_moves::SmoothSymmetricFragmentMover &) –> class protocols::simple_moves::SmoothSymmetricFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);

return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool

yields a length (window_length) of the fragment window to sample from

( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool

yields a start position (window_start) for fragment window to sample from

( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> 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.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ClassicFragmentMover::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>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)

Overloaded function.

1. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
2. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float

C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

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

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

C++: protocols::simple_moves::ClassicFragmentMover::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.simple_moves.SmoothSymmetricFragmentMover) → str

C++: protocols::simple_moves::SmoothSymmetricFragmentMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

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_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> 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_defaults(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

set defaults

C++: protocols::simple_moves::ClassicFragmentMover::set_defaults() –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None

C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothSymmetricFragmentMover

C++: protocols::simple_moves::SmoothSymmetricFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SmoothSymmetricFragmentMover>

show(*args, **kwargs)

Overloaded function.

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

C++: protocols::simple_moves::ClassicFragmentMover::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

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const class std::basic_string<char> &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover to store current residue indices in a map that will be updated as residues are added or deleted, permitting residue indices from the current state to be used to set up movers applied in the future.

__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.simple_moves.StorePoseSnapshot) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, arg0: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) -> 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.simple_moves.StorePoseSnapshot, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply function – actually apply this mover to the pose, modifying the pose.

C++: protocols::simple_moves::StorePoseSnapshot::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, : pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot

C++: protocols::simple_moves::StorePoseSnapshot::operator=(const class protocols::simple_moves::StorePoseSnapshot &) –> class protocols::simple_moves::StorePoseSnapshot &

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.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.moves.Mover

Makea copy of this mover, and return an owning pointer to the copy.

C++: protocols::simple_moves::StorePoseSnapshot::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.simple_moves.StorePoseSnapshot) → pyrosetta.rosetta.protocols.moves.Mover

Create a new instance of this mover, initialized to default settings.

C++: protocols::simple_moves::StorePoseSnapshot::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.simple_moves.StorePoseSnapshot) → str

C++: protocols::simple_moves::StorePoseSnapshot::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

mover_name() → str

C++: protocols::simple_moves::StorePoseSnapshot::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::StorePoseSnapshot::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose_name(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot) → str

Return the name of the reference pose object that will be created and stored in the pose.

C++: protocols::simple_moves::StorePoseSnapshot::reference_pose_name() const –> 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_reference_pose_name(self: pyrosetta.rosetta.protocols.simple_moves.StorePoseSnapshot, name_in: str) → None

Set the name of the reference pose object that will be created and stored in the pose.

C++: protocols::simple_moves::StorePoseSnapshot::set_reference_pose_name(const class std::basic_string<char> &) –> 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.simple_moves.SuperimposeMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Superimpose pose onto reference pose. Default CA only. All residues. Optionally set to superimpose regions or backbone only (N, C, CA, O)

__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.simple_moves.SuperimposeMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, ref_pose: pyrosetta.rosetta.core.pose.Pose, ref_start: int, ref_end: int, target_start: int, target_end: int, CA_only: bool) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) -> 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.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::SuperimposeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, : pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover

C++: protocols::simple_moves::SuperimposeMover::operator=(const class protocols::simple_moves::SuperimposeMover &) –> class protocols::simple_moves::SuperimposeMover &

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.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SuperimposeMover::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.simple_moves.SuperimposeMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SuperimposeMover::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.simple_moves.SuperimposeMover) → str

C++: protocols::simple_moves::SuperimposeMover::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

mover_name() → str

C++: protocols::simple_moves::SuperimposeMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SuperimposeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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_ca_only(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, setting: bool) → None

C++: protocols::simple_moves::SuperimposeMover::set_ca_only(bool) –> 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_reference_pose(*args, **kwargs)

Overloaded function.

1. set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose) -> None
2. set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose, start: int) -> None
3. set_reference_pose(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) -> None

C++: protocols::simple_moves::SuperimposeMover::set_reference_pose(const class core::pose::Pose &, unsigned long, unsigned long) –> void

set_target_range(self: pyrosetta.rosetta.protocols.simple_moves.SuperimposeMover, start: int, end: int) → None

C++: protocols::simple_moves::SuperimposeMover::set_target_range(unsigned long, unsigned long) –> 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.simple_moves.SwitchResidueTypeSetMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

A mover that switches a pose between residue type sets (e.g. centroid and fullatom)

examples:

switch = protocols::simple_moves::SwitchResidueTypeSetMover(“centroid”)

See also:

Pose Residue ResidueType ResidueTypeSet

__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.simple_moves.SwitchResidueTypeSetMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → str

__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.simple_moves.SwitchResidueTypeSetMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Applies ResidueTypeSet converion on the pose

: a single protocols::moves::Mover only converts in ONE direction e.g. to centroid

C++: protocols::simple_moves::SwitchResidueTypeSetMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, : pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover

C++: protocols::simple_moves::SwitchResidueTypeSetMover::operator=(const class protocols::simple_moves::SwitchResidueTypeSetMover &) –> class protocols::simple_moves::SwitchResidueTypeSetMover &

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.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SwitchResidueTypeSetMover::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.simple_moves.SwitchResidueTypeSetMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::SwitchResidueTypeSetMover::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.simple_moves.SwitchResidueTypeSetMover) → str

C++: protocols::simple_moves::SwitchResidueTypeSetMover::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_residue_type_set(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover) → str

C++: protocols::simple_moves::SwitchResidueTypeSetMover::get_residue_type_set() const –> std::string

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

mover_name() → str

C++: protocols::simple_moves::SwitchResidueTypeSetMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::SwitchResidueTypeSetMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

C++: protocols::simple_moves::SwitchResidueTypeSetMover::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

type_set_tag(self: pyrosetta.rosetta.protocols.simple_moves.SwitchResidueTypeSetMover, type_set_tag_in: str) → None

C++: protocols::simple_moves::SwitchResidueTypeSetMover::type_set_tag(const class std::basic_string<char> &) –> void

class pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover

Bases: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover

A SymmetricFragmentMover that applies uniform sampling of fragments

__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.simple_moves.SymmetricFragmentMover, fragset: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, symmetric_residue: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, arg0: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str

__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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
2. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:

mover_3mer.apply(pose)

See also:

ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::simple_moves::SymmetricFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover, : pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover

C++: protocols::simple_moves::SymmetricFragmentMover::operator=(const class protocols::simple_moves::SymmetricFragmentMover &) –> class protocols::simple_moves::SymmetricFragmentMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);

return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool

yields a length (window_length) of the fragment window to sample from

( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool

yields a start position (window_start) for fragment window to sample from

( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> 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.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ClassicFragmentMover::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>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)

Overloaded function.

1. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
2. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float

C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

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

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

C++: protocols::simple_moves::ClassicFragmentMover::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.simple_moves.SymmetricFragmentMover) → str

C++: protocols::simple_moves::SymmetricFragmentMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

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_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> 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_defaults(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

set defaults

C++: protocols::simple_moves::ClassicFragmentMover::set_defaults() –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None

C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SymmetricFragmentMover

C++: protocols::simple_moves::SymmetricFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SymmetricFragmentMover>

show(*args, **kwargs)

Overloaded function.

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

C++: protocols::simple_moves::ClassicFragmentMover::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

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const class std::basic_string<char> &) const –> bool

class pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

this class wraps MinMover, but ensures that its MoveMap always contains up-to-date information about sidechain mobility. It takes its base movemap, allows sidechain freedom at any position mobile in a Factory-generated PackerTask, and passes the new movemap to MinMover. The MinMover’s MoveMap does not accumulate state over many calls to apply().

__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.simple_moves.TaskAwareMinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, minmover_in: pyrosetta.rosetta.protocols.simple_moves.MinMover, factory_in: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover) -> 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.simple_moves.TaskAwareMinMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::TaskAwareMinMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, : pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover) → pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover

C++: protocols::simple_moves::TaskAwareMinMover::operator=(const class protocols::simple_moves::TaskAwareMinMover &) –> class protocols::simple_moves::TaskAwareMinMover &

bb(*args, **kwargs)

Overloaded function.

1. bb(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, val: bool) -> None

C++: protocols::simple_moves::TaskAwareMinMover::bb(bool) –> void

2. bb(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover) -> bool

C++: protocols::simple_moves::TaskAwareMinMover::bb() const –> bool

chi(*args, **kwargs)

Overloaded function.

1. chi(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, val: bool) -> None

C++: protocols::simple_moves::TaskAwareMinMover::chi(bool) –> void

2. chi(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover) -> bool

C++: protocols::simple_moves::TaskAwareMinMover::chi() const –> 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.simple_moves.TaskAwareMinMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::TaskAwareMinMover::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.simple_moves.TaskAwareMinMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::TaskAwareMinMover::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.simple_moves.TaskAwareMinMover) → str

C++: protocols::simple_moves::TaskAwareMinMover::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 > > &

jump(*args, **kwargs)

Overloaded function.

1. jump(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover, j: bool) -> None

C++: protocols::simple_moves::TaskAwareMinMover::jump(const bool) –> void

2. jump(self: pyrosetta.rosetta.protocols.simple_moves.TaskAwareMinMover) -> bool

C++: protocols::simple_moves::TaskAwareMinMover::jump() const –> bool

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

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

mover_name() → str

C++: protocols::simple_moves::TaskAwareMinMover::mover_name() –> std::string

name() → str

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

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::simple_moves::TaskAwareMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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.simple_moves.ThermodynamicData

Bases: pybind11_builtins.pybind11_object

structure that stores data during simulation

intraE and interE are incorrect for now;

__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.simple_moves.ThermodynamicData) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData, arg0: pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData) -> 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.simple_moves.ThermodynamicData, : pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData) → pyrosetta.rosetta.protocols.simple_moves.ThermodynamicData

C++: protocols::simple_moves::ThermodynamicData::operator=(const struct protocols::simple_moves::ThermodynamicData &) –> struct protocols::simple_moves::ThermodynamicData &

class pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

This mover rotates a specific AtomTree Torsion degree of freedom (any valid 4-body torsion). It can rotate by a fixed amount, within a range, or randomly. Optionally, the mover will attempt to internally score the move with MMTorsionEnergy (similar to check_rama in Small/ShearMover). The mover will print a warning message at apply time if the specified DOF is bad. For now this mover only allows one DOF; if you want to have it consider multiple DOF’s that might be a good idea. The DOF is determined by a set of 4 atoms; this allows the mover to check the validity of the DOF. I found it conceptually simpler to think about the 4 atoms involved in the torsion than try to trace DOF_IDs.

__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.simple_moves.TorsionDOFMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, upper: float, lower: float) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID, angle: float) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, arg0: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> 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.simple_moves.TorsionDOFMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::simple_moves::TorsionDOFMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, : pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) → pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover

C++: protocols::simple_moves::TorsionDOFMover::operator=(const class protocols::simple_moves::TorsionDOFMover &) –> class protocols::simple_moves::TorsionDOFMover &

check_mmt(*args, **kwargs)

Overloaded function.

1. check_mmt(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: bool) -> None

(de)activate scoring check

C++: protocols::simple_moves::TorsionDOFMover::check_mmt(const bool) –> void

2. check_mmt(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> bool

getter for scoring check

C++: protocols::simple_moves::TorsionDOFMover::check_mmt() const –> 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>

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_DOF(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → None

return DOF

C++: protocols::simple_moves::TorsionDOFMover::get_DOF(class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &, class core::id::AtomID &) const –> void

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

fpd

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

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

get_angle_range(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, upper: float, lower: float) → None

return range of allowed angles

C++: protocols::simple_moves::TorsionDOFMover::get_angle_range(double &, double &) const –> void

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.simple_moves.TorsionDOFMover) → str

C++: protocols::simple_moves::TorsionDOFMover::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_DOF(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, atom1: pyrosetta.rosetta.core.id.AtomID, atom2: pyrosetta.rosetta.core.id.AtomID, atom3: pyrosetta.rosetta.core.id.AtomID, atom4: pyrosetta.rosetta.core.id.AtomID) → None

change the torsion DOF under consideration

C++: protocols::simple_moves::TorsionDOFMover::set_DOF(const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &, const class core::id::AtomID &) –> void

set_angle_range(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, upper: float, lower: float) → None

///////////////////////////////getters, setters////////////////////////////////////////

set range of desired change - on [180, -180) degrees

C++: protocols::simple_moves::TorsionDOFMover::set_angle_range(const double, const double) –> 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

temp(*args, **kwargs)

Overloaded function.

1. temp(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: float) -> None

set temperature for scoring check

C++: protocols::simple_moves::TorsionDOFMover::temp(const double) –> void

2. temp(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> float

getter for temperature for scoring check

C++: protocols::simple_moves::TorsionDOFMover::temp() const –> double

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

tries(*args, **kwargs)

Overloaded function.

1. tries(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover, setting: int) -> None

set number of tries

C++: protocols::simple_moves::TorsionDOFMover::tries(const unsigned long) –> void

2. tries(self: pyrosetta.rosetta.protocols.simple_moves.TorsionDOFMover) -> int

getter for number of tries

C++: protocols::simple_moves::TorsionDOFMover::tries() const –> unsigned long

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.simple_moves.TrialResult

Bases: pybind11_builtins.pybind11_object

Describes result of a trial

REJECTED : Move was rejected

ACCEPTED : Move was accepted FAILED : Some failure occurred during the move FINISHED : The stopping condition was met

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__(*args, **kwargs)

Overloaded function.

1. __eq__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: pyrosetta.rosetta.protocols.simple_moves.TrialResult) -> bool
2. __eq__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: int) -> bool

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__getstate__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult) → tuple

__gt__

Return self>value.

__hash__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult) → int

__init__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: int) → None

__init_subclass__()

This method is called when a class is subclassed.

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

__int__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult) → int

__le__

Return self<=value.

__lt__

Return self<value.

__ne__(*args, **kwargs)

Overloaded function.

1. __ne__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: pyrosetta.rosetta.protocols.simple_moves.TrialResult) -> bool
2. __ne__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: int) -> bool

__new__()

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

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult) → str

__setattr__

Implement setattr(self, name, value).

__setstate__(self: pyrosetta.rosetta.protocols.simple_moves.TrialResult, arg0: tuple) → None

__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).

class pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Uniform Rotation Mover

__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.simple_moves.UniformRotationMover, alpha: float, axis: pyrosetta.rosetta.numeric.xyzVector_double_t, rb_jump: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover, arg0: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover) -> 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.simple_moves.UniformRotationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply Rotation

Rotate the membrane to the new normal position

C++: protocols::simple_moves::UniformRotationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover, src: pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover) → pyrosetta.rosetta.protocols.simple_moves.UniformRotationMover

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::simple_moves::UniformRotationMover::operator=(const class protocols::simple_moves::UniformRotationMover &) –> class protocols::simple_moves::UniformRotationMover &

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.simple_moves.UniformRotationMover) → str

Get the name of this mover

C++: protocols::simple_moves::UniformRotationMover::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.simple_moves.UniformTranslationMover

Bases: pyrosetta.rosetta.protocols.moves.Mover

Uniform Translation Mover

__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.simple_moves.UniformTranslationMover, new_position_: pyrosetta.rosetta.numeric.xyzVector_double_t, rb_jump: int) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover, arg0: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover) -> 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.simple_moves.UniformTranslationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Apply Translation to membrane position

Translate membrane position to new center

C++: protocols::simple_moves::UniformTranslationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover, src: pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover) → pyrosetta.rosetta.protocols.simple_moves.UniformTranslationMover

Assignment Operator

Make a deep copy of this mover object, overriding the assignment operator

C++: protocols::simple_moves::UniformTranslationMover::operator=(const class protocols::simple_moves::UniformTranslationMover &) –> class protocols::simple_moves::UniformTranslationMover &

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.simple_moves.UniformTranslationMover) → str

Get the name of this mover

C++: protocols::simple_moves::UniformTranslationMover::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.simple_moves.WobbleMover

Bases: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover

A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure

a smooth fragment is chosen according to the FragmentCost Functor;

a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: —-lfff bbb—- f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl—

the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment().

__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.simple_moves.WobbleMover, fragset: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, cost: pyrosetta.rosetta.protocols.simple_moves.FragmentCost) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, fragset: pyrosetta.rosetta.core.fragment.FragSet, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, arg0: pyrosetta.rosetta.protocols.simple_moves.WobbleMover) -> 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__(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → str

__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(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, pos: int) -> bool
2. apply(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> None

Applies classic fragment insertion based on a FragSet

example:

mover_3mer.apply(pose)

See also:

ClassicFragmentMover Pose ConstantLengthFragSet

C++: protocols::simple_moves::ClassicFragmentMover::apply(class core::pose::Pose &) –> void

apply_at_all_positions(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) → int

apply at all movemable positions — honors movemap

C++: protocols::simple_moves::FragmentMover::apply_at_all_positions(class core::pose::Pose &) const –> unsigned long

apply_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, frame: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, movemap: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose) → bool

apply the chosen fragment,

this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

C++: protocols::simple_moves::ClassicFragmentMover::apply_fragment(const class core::fragment::Frame &, unsigned long, const class core::kinematics::MoveMap &, class core::pose::Pose &) const –> bool

assign(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, : pyrosetta.rosetta.protocols.simple_moves.WobbleMover) → pyrosetta.rosetta.protocols.simple_moves.WobbleMover

C++: protocols::simple_moves::WobbleMover::operator=(const class protocols::simple_moves::WobbleMover &) –> class protocols::simple_moves::WobbleMover &

check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

accessor

C++: protocols::simple_moves::ClassicFragmentMover::check_ss() const –> bool

choose_fragment(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.fragment.FrameList, : pyrosetta.rosetta.core.pose.Pose, frame_num: int, frag_num: int) → bool

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num);

return false if nothing suitable is found

C++: protocols::simple_moves::ClassicFragmentMover::choose_fragment(const class core::fragment::FrameList &, const class core::pose::Pose &, unsigned long &, unsigned long &) const –> bool

choose_window_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int) → bool

yields a length (window_length) of the fragment window to sample from

( return false, if no suitable length is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_length(const class core::pose::Pose &, unsigned long &) const –> bool

choose_window_start(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_length: int, window_start: int) → bool

yields a start position (window_start) for fragment window to sample from

( return false, if nothing suitable is found )

C++: protocols::simple_moves::ClassicFragmentMover::choose_window_start(const class core::pose::Pose &, unsigned long, unsigned long &) const –> 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.simple_moves.ClassicFragmentMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::ClassicFragmentMover::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>

define_start_window(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, window_start: int) → None

apply fragment at predefined position

C++: protocols::simple_moves::ClassicFragmentMover::define_start_window(unsigned long) –> void

enable_end_bias_check(*args, **kwargs)

Overloaded function.

1. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) -> None
2. enable_end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) -> None

C++: protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(bool) –> void

end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → float

C++: protocols::simple_moves::ClassicFragmentMover::end_bias() const –> double

end_bias_check(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, : pyrosetta.rosetta.core.pose.Pose, window_start: int) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check(const class core::pose::Pose &, unsigned long) const –> bool

end_bias_check_enabled(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → bool

C++: protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled() const –> bool

fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.core.fragment.FragSet

accessor to the fragment set

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

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

C++: protocols::simple_moves::ClassicFragmentMover::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.simple_moves.WobbleMover) → str

C++: protocols::simple_moves::WobbleMover::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 > > &

initialize(self: pyrosetta.rosetta.protocols.moves.MoveMapMover, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::moves::MoveMapMover::initialize(class core::pose::Pose &) –> void

insert_map(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_map() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

insert_size(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::FragmentMover::insert_size() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

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

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

movemap(*args, **kwargs)

Overloaded function.

1. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, : pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>

2. movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover) -> pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::simple_moves::FragmentMover::movemap() const –> class std::shared_ptr<const class core::kinematics::MoveMap>

name() → str

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

on_new_fragments(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover) → None

is called from set_fragments()

C++: protocols::simple_moves::ClassicFragmentMover::on_new_fragments() –> void

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_buffer_length(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover, setting: int) → None

C++: protocols::simple_moves::WobbleMover::set_buffer_length(unsigned long) –> void

set_check_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: bool) → None

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

C++: protocols::simple_moves::ClassicFragmentMover::set_check_ss(bool) –> 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_defaults(self: pyrosetta.rosetta.protocols.simple_moves.WobbleMover) → None

C++: protocols::simple_moves::WobbleMover::set_defaults() –> void

set_end_bias(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: float) → None

C++: protocols::simple_moves::ClassicFragmentMover::set_end_bias(double) –> void

set_fragments(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, new_frags_: pyrosetta.rosetta.core.fragment.FragSet) → None

setter for the fragment set

C++: protocols::simple_moves::FragmentMover::set_fragments(class std::shared_ptr<const class core::fragment::FragSet>) –> 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_min_frag_length(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_frag_length controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_frag_length(unsigned long) –> void

set_min_overlap(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, setting: int) → None

min_overlap controls the behaviour fragset->region()

C++: protocols::simple_moves::ClassicFragmentMover::set_min_overlap(unsigned long) –> void

set_movemap(self: pyrosetta.rosetta.protocols.simple_moves.FragmentMover, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

setter for the movemap

C++: protocols::simple_moves::FragmentMover::set_movemap(class std::shared_ptr<const class core::kinematics::MoveMap>) –> 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

shared_from_this(self: pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover) → pyrosetta.rosetta.protocols.simple_moves.SmoothFragmentMover

C++: protocols::simple_moves::SmoothFragmentMover::shared_from_this() –> class std::shared_ptr<class protocols::simple_moves::SmoothFragmentMover>

show(*args, **kwargs)

Overloaded function.

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

C++: protocols::simple_moves::ClassicFragmentMover::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

valid_ss(self: pyrosetta.rosetta.protocols.simple_moves.ClassicFragmentMover, new_ss: str) → bool

returns true if the ss string is acceptable

C++: protocols::simple_moves::ClassicFragmentMover::valid_ss(const class std::basic_string<char> &) const –> bool

pyrosetta.rosetta.protocols.simple_moves.replace_file(origfile: str, newfile: str) → None

helper function that safely replaces a file with another

C++: protocols::simple_moves::replace_file(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.simple_moves.setup_vary_polar_hydrogen_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) → None

C++: protocols::simple_moves::setup_vary_polar_hydrogen_geometry(class core::kinematics::MoveMap &, class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>) –> void

pyrosetta.rosetta.protocols.simple_moves.setup_vary_rna_bond_geometry(*args, **kwargs)

Overloaded function.

1. setup_vary_rna_bond_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap) -> None
2. setup_vary_rna_bond_geometry(mm: pyrosetta.rosetta.core.kinematics.MoveMap, pose: pyrosetta.rosetta.core.pose.Pose, atom_level_domain_map: pyrosetta.rosetta.protocols.toolbox.AtomLevelDomainMap, score_type: pyrosetta.rosetta.core.scoring.ScoreType) -> None

C++: protocols::simple_moves::setup_vary_rna_bond_geometry(class core::kinematics::MoveMap &, class core::pose::Pose &, class std::shared_ptr<const class protocols::toolbox::AtomLevelDomainMap>, enum core::scoring::ScoreType) –> void

pyrosetta.rosetta.protocols.simple_moves.uniform_dof_distribution(dof_type: pyrosetta.rosetta.core.id.DOF_Type, num_bins: int, min: float, max: float) → pyrosetta.rosetta.utility.vector1_double

C++: protocols::simple_moves::uniform_dof_distribution(enum core::id::DOF_Type, unsigned long, double, double) –> class utility::vector1<double, class std::allocator<double> >