filter

Bindings for protocols::generalized_kinematic_closure::filter namespace

class pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter

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__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) -> None
  2. __init__(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, arg0: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) -> 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_filter_param(*args, **kwargs)

Overloaded function.

  1. add_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, value: float) -> None

Add a real-valued filter parameter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param(const class std::basic_string<char> &, const double &) –> void

  1. add_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, value: int) -> None

Add a integer-valued filter parameter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param(const class std::basic_string<char> &, const unsigned long) –> void

  1. add_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, value: bool) -> None

Add a Boolean-valued filter parameter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param(const class std::basic_string<char> &, const bool) –> void

  1. add_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, value: str) -> None

Add a string-valued filter parameter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::add_filter_param(const class std::basic_string<char> &, const class std::basic_string<char> &) –> void

apply(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, original_pose: pyrosetta.rosetta.core.pose.Pose, loop_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, tail_residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, atomlist: pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, torsions: pyrosetta.rosetta.utility.vector1_double, bondangles: pyrosetta.rosetta.utility.vector1_double, bondlengths: pyrosetta.rosetta.utility.vector1_double) → bool
Apply this filter to ONE of the kinematic closure solutions produced by the bridgeObjects function,

and return pass or fail.

– The full, initial pose.

– A pose consisting of just the loop to be closed.

– The mapping of (residue index in loop_pose, residue index in original_pose).

– The mapping of (tail residue index in loop_pose, tail residue index in original_pose).

– A list of atoms making the chain that was closed by bridgeObjects, with residue indices corresponding to loop_pose.

– A vector of dihedral angles that the bridgeObjects function spat out.

– A vector of bond angles that the bridgeObjects function spat out.

– A vector of bond lengths that the bridgeObjects function spat out.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> > > > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, : pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::operator=(const class protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter &) –> class protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter &

attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → bool

Gets whether we are attaching a BOINC “ghost” pose observer.

Only does anything in the BOINC graphics build.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::attach_boinc_ghost_observer() const –> bool

binname(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → str

Get the bin name for this filter.

Only used by some filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::binname() const –> std::string

clone(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::clone() const –> class std::shared_ptr<class protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter>

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

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::define_valid_filter_name_enumeration(class utility::tag::XMLSchemaDefinition &) –> void

get_filter_param(*args, **kwargs)

Overloaded function.

  1. get_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, outvalue: float) -> bool

Get a real-valued filter parameter.

Returns false if the parameter couldn’t be found.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param(const class std::basic_string<char> &, double &) const –> bool

  1. get_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, outvalue: int) -> bool

Get a integer-valued filter parameter.

Returns false if the parameter couldn’t be found.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param(const class std::basic_string<char> &, unsigned long &) const –> bool

  1. get_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, outvalue: bool) -> bool

Get a Boolean-valued filter parameter.

Returns false if the parameter couldn’t be found.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param(const class std::basic_string<char> &, bool &) const –> bool

  1. get_filter_param(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, param_name: str, outvalue: str) -> bool

Get a string-valued filter parameter.

Returns false if the parameter couldn’t be found.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_param(const class std::basic_string<char> &, class std::basic_string<char> &) const –> bool

get_filter_type_by_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, filtername: str) → pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type

Given the name of a filter type, return the filter type enum. Returns unknown_filter if not recognized.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_type_by_name(const class std::basic_string<char> &) const –> enum protocols::generalized_kinematic_closure::filter::filter_type

get_filter_type_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, filter_type: int) → str

Given a filter type, return its name. Returns “unknown_filter” if not recognized.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_filter_type_name(const unsigned long) const –> std::string

get_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → str

Returns the name of this class.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_name() const –> std::string

get_this_filter_type_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → str

Gets the filter type name for THIS filter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::get_this_filter_type_name() const –> std::string

load_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, bin_params_file: str) → None

Initializes the BinTransitionCalculator object and loads a bin_params file.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::load_bin_params(const class std::basic_string<char> &) –> void

rama_cutoff_energy(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → float

Get the alpha_aa_rama_check or rama_prepro_check filter’s rama term cutoff energy.

Only used by alpha_aa_rama_check and rama_prepro_check filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::rama_cutoff_energy() const –> double

resnum(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter) → int

Get the residue number that this filter acts on.

Only used by some filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::resnum() const –> unsigned long

set_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, setting: bool) → None

Sets whether we are attaching a BOINC “ghost” pose observer.

Only does anything in the BOINC graphics build.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_attach_boinc_ghost_observer(const bool) –> void

set_binname(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, name_in: str) → None

Set the bin name for this filter.

Only used by some filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_binname(const class std::basic_string<char> &) –> void

set_filter_type(*args, **kwargs)

Overloaded function.

  1. set_filter_type(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, ftype: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type) -> None

Sets the filter type for this filter.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_filter_type(const enum protocols::generalized_kinematic_closure::filter::filter_type &) –> void

  1. set_filter_type(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, ftypename: str) -> None

Sets the filter type for this filter by name.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_filter_type(const class std::basic_string<char> &) –> void

set_rama_cutoff_energy(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, val: float) → None

Set the alpha_aa_rama_check or rama_prepro_check filter’s rama term cutoff energy.

Only used by alpha_aa_rama_check and rama_prepro_check filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_rama_cutoff_energy(const double &) –> void

set_resnum(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.GeneralizedKICfilter, val: int) → None

Set the residue number that this filter acts on.

Only used by some filters.

C++: protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::set_resnum(const unsigned long) –> void