filter

Bindings for protocols::generalized_kinematic_closure::filter namespace

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

Bases: pybind11_object

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 std::string &, const double &) –> void

2. 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 std::string &, const unsigned long) –> void

3. 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 std::string &, const bool) –> void

4. 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 std::string &, const std::string &) –> 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>

static define_valid_filter_name_enumeration(xsd: 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 std::string &, double &) const –> bool

2. 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 std::string &, unsigned long &) const –> bool

3. 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 std::string &, bool &) const –> bool

4. 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 std::string &, std::string &) 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 std::string &) 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 std::string &) –> 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 std::string &) –> 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

2. 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 std::string &) –> 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

class pyrosetta.rosetta.protocols.generalized_kinematic_closure.filter.filter_type

Bases: pybind11_object

Members:

no_filter

loop_bump_check

atom_pair_distance

backbone_bin

alpha_aa_rama_check

rama_prepro_check

unknown_filter

end_of_filter_list

alpha_aa_rama_check = <filter_type.alpha_aa_rama_check: 5>

atom_pair_distance = <filter_type.atom_pair_distance: 3>

backbone_bin = <filter_type.backbone_bin: 4>

end_of_filter_list = <filter_type.unknown_filter: 7>

loop_bump_check = <filter_type.loop_bump_check: 2>

property name

no_filter = <filter_type.no_filter: 1>

rama_prepro_check = <filter_type.rama_prepro_check: 6>

unknown_filter = <filter_type.unknown_filter: 7>

property value