symmetry

Bindings for protocols::simple_moves::symmetry namespace

class pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover

Bases: pyrosetta.rosetta.protocols.moves.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.symmetry.ExtractAsymmetricUnitMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover) -> 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.symmetry.ExtractAsymmetricUnitMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.ExtractAsymmetricUnitMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::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.symmetry.ExtractAsymmetricUnitMover) → str

C++: protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::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::symmetry::ExtractAsymmetricUnitMover::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::symmetry::ExtractAsymmetricUnitMover::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_keep_unknown_aas(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover, keep_unk: bool) → None

If true, residues with aa() == aa_unk will be kept in the asymmetric unit. If false,

residues of aa type aa_unk will be ignored in the conversion and left out of the asymmetric unit.

Desired value for keep_unknown_aas (default=false)

If there are NCAAs in the pose, this must be set to false, or the NCAAs will be

ignored. The keep_unknown_aas defaults to false for historical reasons.

C++: protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::set_keep_unknown_aas(const bool) –> void

set_keep_virtual_residues(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.ExtractAsymmetricUnitMover, keep_virt: bool) → None

if keep_virtual_residues is true, virtual residues will remain in the pose, otherwise

they will be removed

C++: protocols::simple_moves::symmetry::ExtractAsymmetricUnitMover::set_keep_virtual_residues(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_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.symmetry.FaSymDockingSlideTogether

Bases: pyrosetta.rosetta.protocols.moves.Mover

Slides docking partners together by monitoring fa_rep.

If partners are already touching, no change is made. Separation will be 1A or less after calling this 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.symmetry.FaSymDockingSlideTogether, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.FaSymDockingSlideTogether) -> 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.symmetry.FaSymDockingSlideTogether, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.FaSymDockingSlideTogether) → str

C++: protocols::simple_moves::symmetry::FaSymDockingSlideTogether::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.symmetry.NCSResMapping

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

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

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

clone(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::simple_moves::symmetry::NCSResMapping::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_equiv(*args, **kwargs)

Overloaded function.

1. get_equiv(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping, resid: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::simple_moves::symmetry::NCSResMapping::get_equiv(unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

2. get_equiv(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping, groupID: int, resid: int) -> int

C++: protocols::simple_moves::symmetry::NCSResMapping::get_equiv(unsigned long, unsigned long) –> unsigned long

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

ngroups(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping) → int

C++: protocols::simple_moves::symmetry::NCSResMapping::ngroups() –> unsigned long

set_equiv(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.NCSResMapping, group_num: int, res1: int, res2: int) → None

C++: protocols::simple_moves::symmetry::NCSResMapping::set_equiv(unsigned long, unsigned long, unsigned long) –> void

class pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover

Bases: pyrosetta.rosetta.protocols.moves.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.symmetry.SetupForSymmetryMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover, symmdata: pyrosetta.rosetta.core.conformation.symmetry.SymmData) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover, : str) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover) -> 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.symmetry.SetupForSymmetryMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.SetupForSymmetryMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::symmetry::SetupForSymmetryMover::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.symmetry.SetupForSymmetryMover) → str

C++: protocols::simple_moves::symmetry::SetupForSymmetryMover::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::symmetry::SetupForSymmetryMover::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::symmetry::SetupForSymmetryMover::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_preserve_datacache(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover, preserve_cache: bool) → None

Sets whether or not the input asymmetric pose’s datacache should be copied into

the new symmetric pose.

If true, input pose’s datacache is copied into new symmetric pose

If false, input pose’s datacache is cleared (default = false)

C++: protocols::simple_moves::symmetry::SetupForSymmetryMover::set_preserve_datacache(const 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

slide_into_contact(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupForSymmetryMover, val: bool) → None

C++: protocols::simple_moves::symmetry::SetupForSymmetryMover::slide_into_contact(bool) –> 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.symmetry.SetupNCSMover

Bases: pyrosetta.rosetta.protocols.moves.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.symmetry.SetupNCSMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: str, tgt: str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: str, tgt: pyrosetta.rosetta.utility.vector1_std_string) -> None
4. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: pyrosetta.rosetta.utility.vector1_std_string, tgt: pyrosetta.rosetta.utility.vector1_std_string) -> None
5. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) -> 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_group(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: str, tgt: str) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::add_group(class std::basic_string<char>, class std::basic_string<char>) –> void

add_groupD(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: str, tgt: str) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::add_groupD(class std::basic_string<char>, class std::basic_string<char>) –> void

add_groupE(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, src: str, tgt: str) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::add_groupE(class std::basic_string<char>, class std::basic_string<char>) –> void

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

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

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

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

bb(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → bool

C++: protocols::simple_moves::symmetry::SetupNCSMover::bb() –> bool

chi(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → bool

C++: protocols::simple_moves::symmetry::SetupNCSMover::chi() –> 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.symmetry.SetupNCSMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::simple_moves::symmetry::SetupNCSMover::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>

distance_pair(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → bool

C++: protocols::simple_moves::symmetry::SetupNCSMover::distance_pair() –> 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.symmetry.SetupNCSMover) → str

C++: protocols::simple_moves::symmetry::SetupNCSMover::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

limit(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → float

C++: protocols::simple_moves::symmetry::SetupNCSMover::limit() –> double

mover_name() → str

C++: protocols::simple_moves::symmetry::SetupNCSMover::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::symmetry::SetupNCSMover::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

sd(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → float

C++: protocols::simple_moves::symmetry::SetupNCSMover::sd() –> double

set_bb(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, bb_in: bool) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_bb(bool) –> void

set_chi(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, chi_in: bool) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_chi(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.symmetry.SetupNCSMover) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_defaults() –> 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_limit(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, limit_in: float) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_limit(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_sd(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, sd_in: float) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_sd(double) –> void

set_symmetric_sequence(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, symmetric_sequence_in: bool) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_symmetric_sequence(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

set_weight(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover, wt_in: float) → None

C++: protocols::simple_moves::symmetry::SetupNCSMover::set_weight(double) –> 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

symmetric_sequence(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → bool

C++: protocols::simple_moves::symmetry::SetupNCSMover::symmetric_sequence() –> 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

weight(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SetupNCSMover) → float

C++: protocols::simple_moves::symmetry::SetupNCSMover::weight() –> double

class pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact

Bases: pyrosetta.rosetta.protocols.moves.Mover

Contrary to the name, slides things apart first, then together.

__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.symmetry.SymDockingSlideIntoContact) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact, dofs: pyrosetta.rosetta.std.map_unsigned_long_core_conformation_symmetry_SymDof) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymDockingSlideIntoContact) -> 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.symmetry.SymDockingSlideIntoContact, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.SymDockingSlideIntoContact) → str

C++: protocols::simple_moves::symmetry::SymDockingSlideIntoContact::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.symmetry.SymMinMover

Bases: pyrosetta.rosetta.protocols.simple_moves.MinMover

__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.symmetry.SymMinMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover, : str) -> None
3. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover, 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.symmetry.SymMinMover, 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.symmetry.SymMinMover, 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.symmetry.SymMinMover, src: pyrosetta.rosetta.protocols.simple_moves.MinMover) -> None
7. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymMinMover) -> 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.symmetry.SymMinMover, pose_: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.SymMinMover) → pyrosetta.rosetta.protocols.moves.Mover

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

C++: protocols::simple_moves::symmetry::SymMinMover::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.symmetry.SymMinMover) → str

C++: protocols::simple_moves::symmetry::SymMinMover::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::symmetry::SymMinMover::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::symmetry::SymMinMover::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.symmetry.SymmetricRMSMover

Bases: pyrosetta.rosetta.protocols.moves.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.symmetry.SymmetricRMSMover) -> None
2. __init__(self: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover, arg0: pyrosetta.rosetta.protocols.simple_moves.symmetry.SymmetricRMSMover) -> 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.symmetry.SymmetricRMSMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

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

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

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

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.symmetry.SymmetricRMSMover) → str

C++: protocols::simple_moves::symmetry::SymmetricRMSMover::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