matdes¶

Bindings for protocols::matdes namespace

class pyrosetta.rosetta.protocols.matdes.GetRBDOFValues¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE.

__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.

__init__(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> None
__init__(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, jump: int, dof_name: str, verb: bool, ax: str, disp: bool, ang: bool, init_d: float, init_a: float, get_init: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, arg0: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> 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).

angle(*args, **kwargs)¶

Overloaded function.

angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, ang: bool) -> None

C++: protocols::matdes::GetRBDOFValues::angle(const bool) –> void

angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::angle() const –> bool

apply(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::GetRBDOFValues::apply(const class core::pose::Pose &) const –> bool

axis(*args, **kwargs)¶

Overloaded function.

axis(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, ax: str) -> None

C++: protocols::matdes::GetRBDOFValues::axis(const char) –> void

axis(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> str

C++: protocols::matdes::GetRBDOFValues::axis() const –> char

class_name() → str¶: C++: protocols::matdes::GetRBDOFValues::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::GetRBDOFValues::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose, verb: bool, dof_name: str, jump: int, ax: str, disp: bool, ang: bool, init_d: float, init_a: float, get_init: bool) → float¶

get the translation and rotation for a user specified jump

C++: protocols::matdes::GetRBDOFValues::compute(const class core::pose::Pose &, const bool &, const class std::basic_string<char> &, const int &, const char &, const bool &, const bool &, const double &, const double &, const bool &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::GetRBDOFValues::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_init_value(*args, **kwargs)¶

Overloaded function.

get_init_value(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, get_init: bool) -> None

C++: protocols::matdes::GetRBDOFValues::get_init_value(const bool) –> void

get_init_value(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::get_init_value() const –> bool

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

init_angle(*args, **kwargs)¶

Overloaded function.

init_angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, init_a: float) -> None

C++: protocols::matdes::GetRBDOFValues::init_angle(const double) –> void

init_angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> float

C++: protocols::matdes::GetRBDOFValues::init_angle() const –> double

init_disp(*args, **kwargs)¶

Overloaded function.

init_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, init_d: float) -> None

C++: protocols::matdes::GetRBDOFValues::init_disp(const double) –> void

init_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> float

C++: protocols::matdes::GetRBDOFValues::init_disp() const –> double

jump_id(*args, **kwargs)¶

Overloaded function.

jump_id(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, jump: int) -> None

C++: protocols::matdes::GetRBDOFValues::jump_id(const unsigned long) –> void

jump_id(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> int

C++: protocols::matdes::GetRBDOFValues::jump_id() const –> unsigned long

name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → str¶: C++: protocols::matdes::GetRBDOFValues::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::matdes::GetRBDOFValues::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

radial_disp(*args, **kwargs)¶

Overloaded function.

radial_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, disp: bool) -> None

C++: protocols::matdes::GetRBDOFValues::radial_disp(const bool) –> void

radial_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::radial_disp() const –> bool

report(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::GetRBDOFValues::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::GetRBDOFValues::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

sym_dof_name(*args, **kwargs)¶

Overloaded function.

sym_dof_name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, dof_name: str) -> None

C++: protocols::matdes::GetRBDOFValues::sym_dof_name(const class std::basic_string<char> &) –> void

sym_dof_name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> str

C++: protocols::matdes::GetRBDOFValues::sym_dof_name() const –> std::string

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, verb: bool) -> None

C++: protocols::matdes::GetRBDOFValues::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::verbose() const –> bool

class pyrosetta.rosetta.protocols.matdes.SymDofMover¶

Bases: pyrosetta.rosetta.protocols.moves.Mover

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE CLASS SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON. ANY PROTOCOL THAT RELIES ON THIS MOVER IS THREAD-UNSAFE.

__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.

__init__(self: pyrosetta.rosetta.protocols.matdes.SymDofMover) -> None
__init__(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, arg0: pyrosetta.rosetta.protocols.matdes.SymDofMover) -> 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_components_to_pose_if_necessary(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymDofMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, : pyrosetta.rosetta.protocols.matdes.SymDofMover) → pyrosetta.rosetta.protocols.matdes.SymDofMover¶: C++: protocols::matdes::SymDofMover::operator=(const class protocols::matdes::SymDofMover &) –> class protocols::matdes::SymDofMover &

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.matdes.SymDofMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SymDofMover::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.matdes.SymDofMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of object

C++: protocols::matdes::SymDofMover::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.matdes.SymDofMover) → str¶: C++: protocols::matdes::SymDofMover::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::matdes::SymDofMover::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::matdes::SymDofMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

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

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

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

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

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

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

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None¶: C++: protocols::moves::Mover::set_current_tag(const class std::basic_string<char> &) –> void

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

setter for poses contained for rms

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

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

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

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

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None¶: C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)¶

Overloaded function.

show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.

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

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

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.matdes.SymDofMoverSampler¶

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_matdes_SymDofMoverSampler_t

WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED.

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()¶

This method is called when a class is subclassed.

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

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

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

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: 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).

get_angle_diffs(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_angle_diffs() –> class utility::vector1<double, class std::allocator<double> >

get_angles(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_angles() –> class utility::vector1<double, class std::allocator<double> >

get_instance() → protocols::matdes::SymDofMoverSampler¶: C++: utility::SingletonBase<protocols::matdes::SymDofMoverSampler>::get_instance() –> class protocols::matdes::SymDofMoverSampler *

get_radial_disp_diffs(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_radial_disp_diffs() –> class utility::vector1<double, class std::allocator<double> >

get_radial_disps(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_radial_disps() –> class utility::vector1<double, class std::allocator<double> >

get_sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::matdes::SymDofMoverSampler::get_sym_dof_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

set_angle_ranges(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, angles_range_min: pyrosetta.rosetta.utility.vector1_double, angles_range_max: pyrosetta.rosetta.utility.vector1_double, angle_steps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_angle_ranges(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> void

set_angles(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, angles: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_angles(class utility::vector1<double, class std::allocator<double> >) –> void

set_radial_disp_ranges(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, radial_disps_range_min: pyrosetta.rosetta.utility.vector1_double, radial_disps_range_max: pyrosetta.rosetta.utility.vector1_double, radial_disp_steps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_radial_disp_ranges(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> void

set_radial_disps(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, radial_disps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_radial_disps(class utility::vector1<double, class std::allocator<double> >) –> void

set_sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, sym_dof_names: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_sym_dof_names(class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > >) –> void

step(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → None¶: C++: protocols::matdes::SymDofMoverSampler::step() –> void

class pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter¶

Bases: pyrosetta.rosetta.protocols.filters.Filter

filters based on an upper bound # of buried unsatisfied polar residues

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> None
__init__(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, upper_cutoff: int, jump: int, sym_dofs: str, verb: bool, write: bool, mode: str, compare_to_ref: bool, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None
__init__(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, arg0: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> 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.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::SymUnsatHbondFilter::apply(const class core::pose::Pose &) const –> bool

class_name() → str¶: C++: protocols::matdes::SymUnsatHbondFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::SymUnsatHbondFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compare_to_ref(*args, **kwargs)¶

Overloaded function.

compare_to_ref(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, compare_to_ref: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::compare_to_ref(const bool) –> void

compare_to_ref(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::compare_to_ref() const –> bool

compute(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose, verb: bool, write: bool) → float¶: C++: protocols::matdes::SymUnsatHbondFilter::compute(const class core::pose::Pose &, const bool &, const bool &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::SymUnsatHbondFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

jump_num(*args, **kwargs)¶

Overloaded function.

jump_num(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, jump: int) -> None

C++: protocols::matdes::SymUnsatHbondFilter::jump_num(const unsigned long) –> void

jump_num(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> int

C++: protocols::matdes::SymUnsatHbondFilter::jump_num() const –> unsigned long

mode(*args, **kwargs)¶

Overloaded function.

mode(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, mode: str) -> None

C++: protocols::matdes::SymUnsatHbondFilter::mode(const class std::basic_string<char>) –> void

mode(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> str

C++: protocols::matdes::SymUnsatHbondFilter::mode() const –> std::string

name(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → str¶: C++: protocols::matdes::SymUnsatHbondFilter::name() const –> std::string

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::matdes::SymUnsatHbondFilter::reference_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

reference_pose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::matdes::SymUnsatHbondFilter::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

report(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::report(class std::basic_ostream<char> &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::SymUnsatHbondFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const class std::basic_string<char> &) –> void

sym_dof_names(*args, **kwargs)¶

Overloaded function.

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, sym_dofs: str) -> None

C++: protocols::matdes::SymUnsatHbondFilter::sym_dof_names(const class std::basic_string<char>) –> void

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> str

C++: protocols::matdes::SymUnsatHbondFilter::sym_dof_names() const –> std::string

upper_threshold(*args, **kwargs)¶

Overloaded function.

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, upper_cutoff: int) -> None

C++: protocols::matdes::SymUnsatHbondFilter::upper_threshold(const unsigned long) –> void

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> int

C++: protocols::matdes::SymUnsatHbondFilter::upper_threshold() const –> unsigned long

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, verb: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::verbose() const –> bool

write2pdb(*args, **kwargs)¶

Overloaded function.

write2pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, write: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::write2pdb(const bool) –> void

write2pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::write2pdb() const –> bool

write_pymol_string_to_pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pymol_selection: str) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(const class std::basic_string<char>) const –> void

write_to_pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose, mode: str, residue_name: str, residue: int, atom_name: str) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::write_to_pdb(const class core::pose::Pose &, const class std::basic_string<char>, const class std::basic_string<char>, const unsigned long, const class std::basic_string<char>) const –> void