util

Bindings for core::select::util namespace

class pyrosetta.rosetta.core.select.util.SelectResiduesByLayer

Bases: pybind11_object

angle_exponent(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → float

Get the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

C++: core::select::util::SelectResiduesByLayer::angle_exponent() const –> const double &

angle_shift_factor(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → float

Get the shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

C++: core::select::util::SelectResiduesByLayer::angle_shift_factor() const –> const double &

assign(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, : pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → pyrosetta.rosetta.core.select.util.SelectResiduesByLayer

C++: core::select::util::SelectResiduesByLayer::operator=(const class core::select::util::SelectResiduesByLayer &) –> class core::select::util::SelectResiduesByLayer &

clone(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → pyrosetta.rosetta.core.select.util.SelectResiduesByLayer

Clone operator.

Construct a copy of this object and return an owning pointer to the copy.

C++: core::select::util::SelectResiduesByLayer::clone() const –> class std::shared_ptr<class core::select::util::SelectResiduesByLayer>

compute(*args, **kwargs)

Overloaded function.

  1. compute(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_unsigned_long

  2. compute(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str) -> pyrosetta.rosetta.utility.vector1_unsigned_long

  3. compute(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, skip_dssp: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

  4. compute(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, pose: pyrosetta.rosetta.core.pose.Pose, secstruct: str, skip_dssp: bool, asu_only: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

apply

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

dist_exponent(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → float

Get the exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

C++: core::select::util::SelectResiduesByLayer::dist_exponent() const –> const double &

dist_midpoint(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → float

Midpoint of the distance falloff sigmoid.

Defaults to 9.0. Only used by the sidchain_neighbors code.

C++: core::select::util::SelectResiduesByLayer::dist_midpoint() const –> const double &

exclude_aatypes_for_selection(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, aas: pyrosetta.rosetta.utility.vector1_core_chemical_AA) → None

C++: core::select::util::SelectResiduesByLayer::exclude_aatypes_for_selection(const class utility::vector1<enum core::chemical::AA, class std::allocator<enum core::chemical::AA> > &) –> void

initialize(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, burial: float, surface: float) → None

C++: core::select::util::SelectResiduesByLayer::initialize(const double &, const double &) –> void

is_selection_initialized(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → bool

whether the selection has been computed once (it could be stale)

C++: core::select::util::SelectResiduesByLayer::is_selection_initialized() –> bool

layer(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, i: int) → str

return defined layer for each residue

C++: core::select::util::SelectResiduesByLayer::layer(const unsigned long) const –> std::string

make_rasmol_format_file(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, b: bool) → None

accessible surface for evaluating residues are in core or not

C++: core::select::util::SelectResiduesByLayer::make_rasmol_format_file(const bool) –> void

pore_radius(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, ps: float) → None

set pore radius for colculating asa

C++: core::select::util::SelectResiduesByLayer::pore_radius(const double) –> void

restrict_aatypes_for_selection(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, aas: pyrosetta.rosetta.utility.vector1_core_chemical_AA) → None

C++: core::select::util::SelectResiduesByLayer::restrict_aatypes_for_selection(const class utility::vector1<enum core::chemical::AA, class std::allocator<enum core::chemical::AA> > &) –> void

rsd_neighbor_denominator(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → float

Factor by which number of residue neighbors is divided.

Defaults to 1.0. Only used by the sidchain_neighbors code.

C++: core::select::util::SelectResiduesByLayer::rsd_neighbor_denominator() const –> const double &

rsd_sasa(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, i: int) → float

accessbile surface are of each residue

C++: core::select::util::SelectResiduesByLayer::rsd_sasa(const unsigned long) const –> double

sasa_core(*args, **kwargs)

Overloaded function.

  1. sasa_core(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, r: float) -> None

  2. sasa_core(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, r: float, ss: str) -> None

accessible surface for evaluating residues are in core or not

C++: core::select::util::SelectResiduesByLayer::sasa_core(const double &, const std::string &) –> void

sasa_surface(*args, **kwargs)

Overloaded function.

  1. sasa_surface(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, r: float) -> None

  2. sasa_surface(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, r: float, ss: str) -> None

accessible surface for evaluating residues are in surface or not

C++: core::select::util::SelectResiduesByLayer::sasa_surface(const double &, const std::string &) –> void

selected_boundary_residues(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → pyrosetta.rosetta.utility.vector1_unsigned_long

selected residues on boundary

C++: core::select::util::SelectResiduesByLayer::selected_boundary_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

selected_core_residues(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → pyrosetta.rosetta.utility.vector1_unsigned_long

selected residues in core

C++: core::select::util::SelectResiduesByLayer::selected_core_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

selected_surface_residues(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) → pyrosetta.rosetta.utility.vector1_unsigned_long

selected residues on surface

C++: core::select::util::SelectResiduesByLayer::selected_surface_residues() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

set_angle_exponent(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, val: float) → None

Set the exponent for the angle term, which affects how close other atoms have to be to the CA-CB line to be counted fully.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor is then added, and the resulting value is raised to the angle_exponent (default 2.0) and multiplied by the distance factor.

C++: core::select::util::SelectResiduesByLayer::set_angle_exponent(const double &) –> void

set_angle_shift_factor(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, val: float) → None

Set the shift factor for the angle term.

Residues in the cone are counted and the count is multiplied by the cosine of the angle between the CA-CB vector and the CA-other atom vector. The shift factor (default 0.5) is then added, and the resulting value is raised to the angle_exponent and multiplied by the distance factor.

C++: core::select::util::SelectResiduesByLayer::set_angle_shift_factor(const double &) –> void

set_design_layer(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, pick_core: bool, pick_boundary: bool, pick_surface: bool) → None

C++: core::select::util::SelectResiduesByLayer::set_design_layer(const bool, const bool, const bool) –> void

set_dist_exponent(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, val: float) → None

Set the exponent for the distance term, which affects how sharp the falloff is with distance.

The distance term is: 1/(1+exp(n*(d - m))), where d is the distance, n is the exponent set by this term, and m is the midpoint of the falloff. The n value sets the sharpness. Defaults to 1.0.

C++: core::select::util::SelectResiduesByLayer::set_dist_exponent(const double &) –> void

set_dist_midpoint(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, val: float) → None

Set the midpoint of the distance falloff sigmoid.

C++: core::select::util::SelectResiduesByLayer::set_dist_midpoint(const double &) –> void

set_rsd_neighbor_denominator(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, val: float) → None

Set the value by which the number of residue neighbors is divided.

C++: core::select::util::SelectResiduesByLayer::set_rsd_neighbor_denominator(const double &) –> void

use_sidechain_neighbors(*args, **kwargs)

Overloaded function.

  1. use_sidechain_neighbors(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer, b: bool) -> None

C++: core::select::util::SelectResiduesByLayer::use_sidechain_neighbors(const bool) –> void

  1. use_sidechain_neighbors(self: pyrosetta.rosetta.core.select.util.SelectResiduesByLayer) -> bool

C++: core::select::util::SelectResiduesByLayer::use_sidechain_neighbors() const –> bool

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> >

  1. 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> >

  1. 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> >

  1. 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.calc_sc_neighbors(*args, **kwargs)

Overloaded function.

  1. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_double

  2. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float) -> pyrosetta.rosetta.utility.vector1_double

  3. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float) -> pyrosetta.rosetta.utility.vector1_double

  4. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float, dist_exponent: float) -> pyrosetta.rosetta.utility.vector1_double

  5. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float, dist_exponent: float, dist_midpoint: float) -> pyrosetta.rosetta.utility.vector1_double

  6. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float, dist_exponent: float, dist_midpoint: float, res_denominator: float) -> pyrosetta.rosetta.utility.vector1_double

  7. calc_sc_neighbors(pose: pyrosetta.rosetta.core.pose.Pose, angle_exponent: float, angle_shift_factor: float, dist_exponent: float, dist_midpoint: float, res_denominator: float, asu_only: bool) -> pyrosetta.rosetta.utility.vector1_double

Calculate SC neighbors using cones. Code used for LayerSelector.

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::calc_sc_neighbors(const class core::pose::Pose &, const double, const double, const double, const double, const double, const bool) –> class utility::vector1<double, class std::allocator<double> >

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

pyrosetta.rosetta.core.select.util.res1_pointed_at_res2(res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, angle_cutoff: float, dist_cutoff: float) → bool

figures out if res1 and res2 are pointing at eachother

the angle is the max angle between the two residues, dist_cutoff is how far the coords are from eachother

C++: core::select::util::res1_pointed_at_res2(const class core::conformation::Residue &, const class core::conformation::Residue &, const double, const double) –> bool