| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.select.util.SelectResiduesByLayer) -> NoneType
2. __init__(self : rosetta.core.select.util.SelectResiduesByLayer, src : rosetta.core.select.util.SelectResiduesByLayer) -> NoneType
3. __init__(self : rosetta.core.select.util.SelectResiduesByLayer, pick_core : bool, pick_boundary : bool, pick_surface : bool) -> NoneType
4. __init__(self : rosetta.core.select.util.SelectResiduesByLayer, pick : str) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- angle_exponent(...) from builtins.PyCapsule
- angle_exponent(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.
- angle_shift_factor(...) from builtins.PyCapsule
- angle_shift_factor(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.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.select.util.SelectResiduesByLayer, : rosetta.core.select.util.SelectResiduesByLayer) -> rosetta.core.select.util.SelectResiduesByLayer
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.select.util.SelectResiduesByLayer) -> rosetta.core.select.util.SelectResiduesByLayer
Clone operator.
Construct a copy of this object and return an owning pointer to the copy.
- compute(...) from builtins.PyCapsule
- compute(*args, **kwargs)
Overloaded function.
1. compute(self : rosetta.core.select.util.SelectResiduesByLayer, pose : rosetta.core.pose.Pose) -> rosetta.utility.vector1_unsigned_long
apply
2. compute(self : rosetta.core.select.util.SelectResiduesByLayer, pose : rosetta.core.pose.Pose, secstruct : str) -> rosetta.utility.vector1_unsigned_long
apply
3. compute(self : rosetta.core.select.util.SelectResiduesByLayer, pose : rosetta.core.pose.Pose, secstruct : str, skip_dssp : bool) -> rosetta.utility.vector1_unsigned_long
apply
- dist_exponent(...) from builtins.PyCapsule
- dist_exponent(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.
- dist_midpoint(...) from builtins.PyCapsule
- dist_midpoint(rosetta.core.select.util.SelectResiduesByLayer) -> float
Midpoint of the distance falloff sigmoid.
Defaults to 9.0. Only used by the sidchain_neighbors code.
- exclude_aatypes_for_selection(...) from builtins.PyCapsule
- exclude_aatypes_for_selection(self : rosetta.core.select.util.SelectResiduesByLayer, aas : rosetta.utility.vector1_core_chemical_AA) -> NoneType
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.core.select.util.SelectResiduesByLayer, burial : float, surface : float) -> NoneType
- is_selection_initialized(...) from builtins.PyCapsule
- is_selection_initialized(rosetta.core.select.util.SelectResiduesByLayer) -> bool
whether the selection has been computed once (it could be stale)
- layer(...) from builtins.PyCapsule
- layer(self : rosetta.core.select.util.SelectResiduesByLayer, i : int) -> str
return defined layer for each residue
- make_rasmol_format_file(...) from builtins.PyCapsule
- make_rasmol_format_file(self : rosetta.core.select.util.SelectResiduesByLayer, b : bool) -> NoneType
accessible surface for evaluating residues are in core or not
- pore_radius(...) from builtins.PyCapsule
- pore_radius(self : rosetta.core.select.util.SelectResiduesByLayer, ps : float) -> NoneType
set pore radius for colculating asa
- restrict_aatypes_for_selection(...) from builtins.PyCapsule
- restrict_aatypes_for_selection(self : rosetta.core.select.util.SelectResiduesByLayer, aas : rosetta.utility.vector1_core_chemical_AA) -> NoneType
- rsd_neighbor_denominator(...) from builtins.PyCapsule
- rsd_neighbor_denominator(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.
- rsd_sasa(...) from builtins.PyCapsule
- rsd_sasa(self : rosetta.core.select.util.SelectResiduesByLayer, i : int) -> float
accessbile surface are of each residue
- sasa_core(...) from builtins.PyCapsule
- sasa_core(*args, **kwargs)
Overloaded function.
1. sasa_core(self : rosetta.core.select.util.SelectResiduesByLayer, r : float) -> NoneType
accessible surface for evaluating residues are in core or not
2. sasa_core(self : rosetta.core.select.util.SelectResiduesByLayer, r : float, ss : str) -> NoneType
accessible surface for evaluating residues are in core or not
- sasa_surface(...) from builtins.PyCapsule
- sasa_surface(*args, **kwargs)
Overloaded function.
1. sasa_surface(self : rosetta.core.select.util.SelectResiduesByLayer, r : float) -> NoneType
accessible surface for evaluating residues are in surface or not
2. sasa_surface(self : rosetta.core.select.util.SelectResiduesByLayer, r : float, ss : str) -> NoneType
accessible surface for evaluating residues are in surface or not
- selected_boundary_residues(...) from builtins.PyCapsule
- selected_boundary_residues(rosetta.core.select.util.SelectResiduesByLayer) -> rosetta.utility.vector1_unsigned_long
selected residues on boundary
- selected_core_residues(...) from builtins.PyCapsule
- selected_core_residues(rosetta.core.select.util.SelectResiduesByLayer) -> rosetta.utility.vector1_unsigned_long
selected residues in core
- selected_surface_residues(...) from builtins.PyCapsule
- selected_surface_residues(rosetta.core.select.util.SelectResiduesByLayer) -> rosetta.utility.vector1_unsigned_long
selected residues on surface
- set_angle_exponent(...) from builtins.PyCapsule
- set_angle_exponent(self : rosetta.core.select.util.SelectResiduesByLayer, val : float) -> NoneType
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.
- set_angle_shift_factor(...) from builtins.PyCapsule
- set_angle_shift_factor(self : rosetta.core.select.util.SelectResiduesByLayer, val : float) -> NoneType
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.
- set_design_layer(...) from builtins.PyCapsule
- set_design_layer(self : rosetta.core.select.util.SelectResiduesByLayer, pick_core : bool, pick_boundary : bool, pick_surface : bool) -> NoneType
- set_dist_exponent(...) from builtins.PyCapsule
- set_dist_exponent(self : rosetta.core.select.util.SelectResiduesByLayer, val : float) -> NoneType
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.
- set_dist_midpoint(...) from builtins.PyCapsule
- set_dist_midpoint(self : rosetta.core.select.util.SelectResiduesByLayer, val : float) -> NoneType
Set the midpoint of the distance falloff sigmoid.
- set_rsd_neighbor_denominator(...) from builtins.PyCapsule
- set_rsd_neighbor_denominator(self : rosetta.core.select.util.SelectResiduesByLayer, val : float) -> NoneType
Set the value by which the number of residue neighbors is divided.
- use_sidechain_neighbors(...) from builtins.PyCapsule
- use_sidechain_neighbors(*args, **kwargs)
Overloaded function.
1. use_sidechain_neighbors(self : rosetta.core.select.util.SelectResiduesByLayer, b : bool) -> NoneType
2. use_sidechain_neighbors(rosetta.core.select.util.SelectResiduesByLayer) -> bool
|