pack_daemon

Bindings for protocols::pack_daemon namespace

class pyrosetta.rosetta.protocols.pack_daemon.InSetExpression

Bases: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression

Returns “true” if the expression ex evaluates to one of a set of indicated values.

__call__(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression) → float

C++: protocols::pack_daemon::InSetExpression::operator()() const –> double

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → 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).

active_variables(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: numeric::expression_parser::UnaryExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, : pyrosetta.rosetta.protocols.pack_daemon.InSetExpression) → pyrosetta.rosetta.protocols.pack_daemon.InSetExpression

C++: protocols::pack_daemon::InSetExpression::operator=(const class protocols::pack_daemon::InSetExpression &) –> class protocols::pack_daemon::InSetExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::InSetExpression::differentiate(const class std::basic_string<char> &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

ex(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::UnaryExpression::ex() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_expression(self: pyrosetta.rosetta.numeric.expression_parser.UnaryExpression, ex: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::UnaryExpression::set_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

value_set(self: pyrosetta.rosetta.protocols.pack_daemon.InSetExpression, values: pyrosetta.rosetta.utility.vector1_double) → None

C++: protocols::pack_daemon::InSetExpression::value_set(const class utility::vector1<double, class std::allocator<double> > &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator

Bases: pybind11_builtins.pybind11_object

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator) → 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.pack_daemon.NPDPropCalculator, : pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator) → pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator

C++: protocols::pack_daemon::NPDPropCalculator::operator=(const class protocols::pack_daemon::NPDPropCalculator &) –> class protocols::pack_daemon::NPDPropCalculator &

calculate(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator, p: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::pack_daemon::NPDPropCalculator::calculate(const class core::pose::Pose &) –> double

setup(self: pyrosetta.rosetta.protocols.pack_daemon.NPDPropCalculator, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::NPDPropCalculator::setup(const class core::pose::Pose &, const class core::pack::task::PackerTask &) –> void

class pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker

Bases: pybind11_builtins.pybind11_object

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, ig: pyrosetta.rosetta.core.pack.interaction_graph.FixedBBInteractionGraph, rot_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → 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.pack_daemon.QuickRepacker, : pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker) → pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker

C++: protocols::pack_daemon::QuickRepacker::operator=(const class protocols::pack_daemon::QuickRepacker &) –> class protocols::pack_daemon::QuickRepacker &

repack(self: pyrosetta.rosetta.protocols.pack_daemon.QuickRepacker, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) → Tuple[pyrosetta.rosetta.utility.vector1_int, float]

C++: protocols::pack_daemon::QuickRepacker::repack(const class utility::vector0<int, class std::allocator<int> > &) –> struct std::pair<class utility::vector1<int, class std::allocator<int> >, double>

class pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression

Bases: pyrosetta.rosetta.numeric.expression_parser.VariableExpression

Stores the result of the surragate expression as if this expression were a variable, but defers to the root expression for questions of deriviatives and which variables are active (this is not a real variable).

__call__(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression) → float

C++: numeric::expression_parser::VariableExpression::operator()() const –> double

__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.pack_daemon.SurrogateVariableExpression, : str) -> None
2. __init__(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, : str, value: float) -> None
3. __init__(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, arg0: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression) -> 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).

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: protocols::pack_daemon::SurrogateVariableExpression::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, : pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression) → pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression

C++: protocols::pack_daemon::SurrogateVariableExpression::operator=(const class protocols::pack_daemon::SurrogateVariableExpression &) –> class protocols::pack_daemon::SurrogateVariableExpression &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::SurrogateVariableExpression::differentiate(const class std::basic_string<char> &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

name(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression) → str

C++: numeric::expression_parser::VariableExpression::name() const –> std::string

root_expression(self: pyrosetta.rosetta.protocols.pack_daemon.SurrogateVariableExpression, setting: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: protocols::pack_daemon::SurrogateVariableExpression::root_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_value(self: pyrosetta.rosetta.numeric.expression_parser.VariableExpression, value: float) → None

C++: numeric::expression_parser::VariableExpression::set_value(double) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VMaxBy

Bases: pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2

Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the largest value in expression 1

__call__(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy) → float

C++: protocols::pack_daemon::VMaxBy::operator()() const –> double

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy, ex1: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, ex2: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → 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).

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: protocols::pack_daemon::VMaxBy::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy, : pyrosetta.rosetta.protocols.pack_daemon.VMaxBy) → pyrosetta.rosetta.protocols.pack_daemon.VMaxBy

C++: protocols::pack_daemon::VMaxBy::operator=(const class protocols::pack_daemon::VMaxBy &) –> class protocols::pack_daemon::VMaxBy &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMaxBy, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMaxBy::differentiate(const class std::basic_string<char> &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

class pyrosetta.rosetta.protocols.pack_daemon.VMinBy

Bases: pyrosetta.rosetta.protocols.pack_daemon.VectorFunction2

Take two vector expressions of equal length; returns the value from position i in expression 2 where position i is the position with the smallest value in expression 1

__call__(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy) → float

C++: protocols::pack_daemon::VMinBy::operator()() const –> double

__delattr__

Implement delattr(self, name).

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy, ex1: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression, ex2: pyrosetta.rosetta.protocols.pack_daemon.VectorExpression) → 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).

active_variables(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy) → pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

C++: protocols::pack_daemon::VMinBy::active_variables() const –> class std::list<std::string, class std::allocator<std::string > >

assign(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy, : pyrosetta.rosetta.protocols.pack_daemon.VMinBy) → pyrosetta.rosetta.protocols.pack_daemon.VMinBy

C++: protocols::pack_daemon::VMinBy::operator=(const class protocols::pack_daemon::VMinBy &) –> class protocols::pack_daemon::VMinBy &

differentiate(self: pyrosetta.rosetta.protocols.pack_daemon.VMinBy, varname: str) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: protocols::pack_daemon::VMinBy::differentiate(const class std::basic_string<char> &) const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e1(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e1() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

e2(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression) → pyrosetta.rosetta.numeric.expression_parser.Expression

C++: numeric::expression_parser::BinaryExpression::e2() const –> class std::shared_ptr<const class numeric::expression_parser::Expression>

set_first_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e1: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_first_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

set_second_expression(self: pyrosetta.rosetta.numeric.expression_parser.BinaryExpression, e2: pyrosetta.rosetta.numeric.expression_parser.Expression) → None

C++: numeric::expression_parser::BinaryExpression::set_second_expression(class std::shared_ptr<const class numeric::expression_parser::Expression>) –> void

pyrosetta.rosetta.protocols.pack_daemon.create_entity_resfile_contents(resfile: pyrosetta.rosetta.std.istream, resfile_name: str, entity_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, entity_task: pyrosetta.rosetta.core.pack.task.PackerTask, num_entities: int) → None

C++: protocols::pack_daemon::create_entity_resfile_contents(class std::basic_istream<char> &, const class std::basic_string<char> &, class std::shared_ptr<class core::pack::task::ResfileContents> &, class std::shared_ptr<class core::pack::task::PackerTask> &, unsigned long &) –> void

pyrosetta.rosetta.protocols.pack_daemon.initialize_ga_randomizer_from_entity_task(rand: pyrosetta.rosetta.protocols.genetic_algorithm.PositionSpecificRandomizer, entity_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::initialize_ga_randomizer_from_entity_task(class std::shared_ptr<class protocols::genetic_algorithm::PositionSpecificRandomizer>, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.protocols.pack_daemon.initialize_task_from_entity_resfile_and_secondary_resfile(pose: pyrosetta.rosetta.core.pose.Pose, ec: pyrosetta.rosetta.protocols.pack_daemon.EntityCorrespondence, entity_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, secondary_resfile_contents: pyrosetta.rosetta.core.pack.task.ResfileContents, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile(const class core::pose::Pose &, class std::shared_ptr<const class protocols::pack_daemon::EntityCorrespondence>, const class core::pack::task::ResfileContents &, const class core::pack::task::ResfileContents &, class std::shared_ptr<class core::pack::task::PackerTask>) –> void