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- builtins.object
-
- GeneralizedKICperturber
- perturber_effect
class GeneralizedKICperturber(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> NoneType
2. __init__(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, src : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_atom_set(...) from builtins.PyCapsule
- add_atom_set(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, atomset : rosetta.utility.vector1_core_id_NamedAtomID) -> NoneType
Adds a set of atoms defining a bond length, bond angle, or dihedral
angle to the list of sets of atoms on which this perturber should act.
These are indices based on the original structure, NOT based on
the loop to be closed. Some effects act on a list of residues, while
others act on a list of atoms.
- add_inputvalue(...) from builtins.PyCapsule
- add_inputvalue(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, inputvalue : float) -> NoneType
Adds a real value to the list of real input values.
- add_residue(...) from builtins.PyCapsule
- add_residue(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, residue_index : int) -> NoneType
Adds a residue to the list of residues on which this perturber should act.
These are indices based on the original structure, NOT based on
the loop to be closed. Some effects act on a list of residues, while
others act on a list of AtomIDs.
- apply(...) from builtins.PyCapsule
- apply(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, original_pose : rosetta.core.pose.Pose, loop_pose : rosetta.core.pose.Pose, residue_map : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, tail_residue_map : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, atomlist : rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, torsions : rosetta.utility.vector1_double, bondangles : rosetta.utility.vector1_double, bondlengths : rosetta.utility.vector1_double) -> NoneType
Applies the perturbation to the vectors of desired torsions, desired angles, and desired bond lengths.
- The original pose.
- A pose consisting of just the loop to be perturbed, plus one residue on each side establishing the frame.
- Mapping of (loop residue, original pose residue).
- Mapping of (tail residue in loop pose, original pose tail residue).
- List of atoms (residue indices are based on the loop_pose).
- Desired torsions for each atom; can be set or altered by the apply() function.
- Desired bond angles for each atom; can be set or altered by the apply() function.
- Desired bond lengths for each atom; can be set or altered by the apply() function.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber
- attach_boinc_ghost_observer(...) from builtins.PyCapsule
- attach_boinc_ghost_observer(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> bool
Gets whether we are attaching a BOINC "ghost" pose observer.
Only does anything in the BOINC graphics build.
- bin(...) from builtins.PyCapsule
- bin(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> str
Get the bin that the set_backbone_bin perturber will use.
- clear_residues(...) from builtins.PyCapsule
- clear_residues(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> NoneType
Clears the residue list for this perturber
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber
- custom_rama_table(...) from builtins.PyCapsule
- custom_rama_table(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> rosetta.core.scoring.Rama_Table_Type
Get the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.
- get_name(...) from builtins.PyCapsule
- get_name(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> str
- get_perturber_effect(...) from builtins.PyCapsule
- get_perturber_effect(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect
Returns the enum type for the effect of this perturber.
- get_perturber_effect_from_name(...) from builtins.PyCapsule
- get_perturber_effect_from_name(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, name : str) -> rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect
Returns the enum type for the effect of a pertuber based on a perturber name.
Returns unknown_effect if can't find a match for the name.
- get_perturber_effect_name(...) from builtins.PyCapsule
- get_perturber_effect_name(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, effect : int) -> str
Returns the name of a perturber given the enum type.
Returns "unknown_effect" if no such effect exists.
- init_bbgmover(...) from builtins.PyCapsule
- init_bbgmover(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, loop_pose : rosetta.core.pose.Pose, residue_map : rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) -> NoneType
- iterations(...) from builtins.PyCapsule
- iterations(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> int
Return the number of iterations for this perturber
- load_bin_params(...) from builtins.PyCapsule
- load_bin_params(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, bin_params_file : str) -> NoneType
Initializes the BinTransitionCalculator object and loads a bin_params file.
- must_switch_bins(...) from builtins.PyCapsule
- must_switch_bins(rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) -> bool
Return whether the perturb_backbone_by_bins perturber requires residues to change their torsion
bins every move, or whether they can stay within the same bin.
- set_attach_boinc_ghost_observer(...) from builtins.PyCapsule
- set_attach_boinc_ghost_observer(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, setting : bool) -> NoneType
Sets whether we are attaching a BOINC "ghost" pose observer.
Only does anything in the BOINC graphics build.
- set_bin(...) from builtins.PyCapsule
- set_bin(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, bin : str) -> NoneType
Set the bin that the set_backbone_bin perturber will use.
- set_custom_rama_table(...) from builtins.PyCapsule
- set_custom_rama_table(*args, **kwargs)
Overloaded function.
1. set_custom_rama_table(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, type : rosetta.core.scoring.Rama_Table_Type) -> NoneType
Set the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.
2. set_custom_rama_table(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, name : str) -> NoneType
Set the custom Ramachandran table (by name) for the perturb_alpha_backbone_by_rama perturber.
- set_iterations(...) from builtins.PyCapsule
- set_iterations(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, val : int) -> NoneType
Set the number of iterations for this perturber
- set_must_switch_bins(...) from builtins.PyCapsule
- set_must_switch_bins(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, val : bool) -> NoneType
Set whether the perturb_backbone_by_bins perturber requires residues to change their torsion
bins every move, or whether they can stay within the same bin.
- set_perturber_effect(...) from builtins.PyCapsule
- set_perturber_effect(*args, **kwargs)
Overloaded function.
1. set_perturber_effect(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, effect : rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> NoneType
Sets the effect of this perturber.
2. set_perturber_effect(self : rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, effectname : str) -> NoneType
Sets the effect of this perturber using the perturber effect name.
Exits with an error message if the name is unknown.
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class perturber_effect(builtins.object) |
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The effect of the perturber (e.g. randomizing alpha-amino acid phi/psi angles, altering side-chains, etc.)
Perturbation effects starting with "set" set parameters to defined values (e.g. set the third phi angle
to 45 degrees). Perturbation effects starting with "randomize" set parameters based on random
distributions, with no consideration of the initial value. Perturbation effects starting with "jitter"
set parameters to some new value based on a random distribution about the initial value.
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect, rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect, int) -> NoneType
2. __init__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect, rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> bool
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- __repr__(...) from builtins.PyCapsule
- __repr__(rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> str
Data and other attributes defined here:
- end_of_effect_list = perturber_effect.end_of_effect_list
- no_effect = perturber_effect.no_effect
- perturb_backbone_by_bins = perturber_effect.perturb_backbone_by_bins
- perturb_dihedral = perturber_effect.perturb_dihedral
- perturb_dihedral_bbg = perturber_effect.perturb_dihedral_bbg
- randomize_alpha_backbone_by_rama = perturber_effect.randomize_alpha_backbone_by_rama
- randomize_backbone_by_bins = perturber_effect.randomize_backbone_by_bins
- randomize_dihedral = perturber_effect.randomize_dihedral
- sample_cis_peptide_bond = perturber_effect.sample_cis_peptide_bond
- set_backbone_bin = perturber_effect.set_backbone_bin
- set_bondangle = perturber_effect.set_bondangle
- set_bondlength = perturber_effect.set_bondlength
- set_dihedral = perturber_effect.set_dihedral
- unknown_effect = perturber_effect.end_of_effect_list
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