util

Bindings for core::select::util namespace

pyrosetta.rosetta.core.select.util.calc_interacting_vector(pose: pyrosetta.rosetta.core.pose.Pose, part1res: pyrosetta.rosetta.std.set_unsigned_long_t, part2res: pyrosetta.rosetta.std.set_unsigned_long_t, CB_dist_cutoff: float, nearby_atom_cutoff: float, vector_angle_cutoff: float, vector_dist_cutoff: float) → pyrosetta.rosetta.utility.vector1_bool

calculate the same thing but don’t require an interface

C++: core::select::util::calc_interacting_vector(const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const double, const double, const double, const double) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.util.calc_interface_vector(*args, **kwargs)

Overloaded function.

1. calc_interface_vector(pose: pyrosetta.rosetta.core.pose.Pose, chain1_number: int, chain2_number: int) -> pyrosetta.rosetta.utility.vector1_bool

minimal chain number definition

C++: core::select::util::calc_interface_vector(const class core::pose::Pose &, const unsigned long, const unsigned long) –> class utility::vector1<bool, class std::allocator<bool> >

2. calc_interface_vector(pose: pyrosetta.rosetta.core.pose.Pose, chain1_number: int, chain2_number: int, CB_dist_cutoff: float, nearby_atom_cutoff: float, vector_angle_cutoff: float, vector_dist_cutoff: float) -> pyrosetta.rosetta.utility.vector1_bool

full runner that takes all of the inputs for chains

C++: core::select::util::calc_interface_vector(const class core::pose::Pose &, const unsigned long, const unsigned long, const double, const double, const double, const double) –> class utility::vector1<bool, class std::allocator<bool> >

3. calc_interface_vector(pose: pyrosetta.rosetta.core.pose.Pose, interface_jump: int, CB_dist_cutoff: float, nearby_atom_cutoff: float, vector_angle_cutoff: float, vector_dist_cutoff: float) -> pyrosetta.rosetta.utility.vector1_bool

full runner that takes the jump

C++: core::select::util::calc_interface_vector(const class core::pose::Pose &, const int, const double, const double, const double, const double) –> class utility::vector1<bool, class std::allocator<bool> >

4. calc_interface_vector(pose: pyrosetta.rosetta.core.pose.Pose, interface_jump: int) -> pyrosetta.rosetta.utility.vector1_bool

minimal jump runner

C++: core::select::util::calc_interface_vector(const class core::pose::Pose &, const int) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.util.calculate_point_in_cone(point_coordinates: pyrosetta.rosetta.numeric.xyzVector_double_t, conevect: pyrosetta.rosetta.numeric.xyzVector_double_t, conevect_coordinate_2: pyrosetta.rosetta.numeric.xyzVector_double_t, angle_exponent: float, angle_shift_factor: float, dist_exponent: float, dist_midpoint: float) → float

Given a point in 3D space, and a vector and floats defining a cone, determine the extent to which the point

is in the cone.

The return value ranges from 0 (not in the cone) to 1 (fully in the cone). The cone has fuzzy boundaries, so non-integer return values are possible.

The coordinates of a test point that may or may not be in the cone. For the layer selector, this is the beta- or alpha-carbon of another residue.

A vector defining the direction in which the test cone opens. For the layer selector, this is the CA-CB vector of an amino acid.

The coordinate in space of the base of the cone. For the layer selector, this is the CB atom.

A value defining how rapidly the cone falls off in the angular direction.

A value that shifts the angluar falloff.

A value defining how rapidly the cone falls off with distance.

A value defining the midpoint of the distance falloff.

C++: core::select::util::calculate_point_in_cone(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const double, const double, const double, const double) –> double

pyrosetta.rosetta.core.select.util.determine_whether_point_is_buried(point_coordinates: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float, dist_exponent: float, dist_midpoint: float, burial_threshold: float) → bool

Given a point in 3D space, determine whether or not that point is buried by the method of sidechain neighbor cones.

A crude distance cutoff metric is also used to make this calculation more efficient.

Returns true for burial, false otherwise.

The 3D coordinates of the point in space.

The pose, for reference.

A value defining how rapidly the cone falls off in the angular direction.

A value that shifts the angluar falloff.

A value defining how rapidly the cone falls off with distance.

A value defining the midpoint of the distance falloff.

The cutoff for considering a point to be buried. Roughly, this is the number of cones that the point must be inside in order to consider it “buried”.

C++: core::select::util::determine_whether_point_is_buried(const class numeric::xyzVector<double> &, const class core::pose::Pose &, const double, const double, const double, const double, const double) –> bool