perturber

Bindings for protocols::generalized_kinematic_closure::perturber namespace

class pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GenKICPerturberEffect

Bases: pybind11_builtins.pybind11_object

Members:

set

randomize

perturb

property name
perturb = <GenKICPerturberEffect.perturb: 3>
randomize = <GenKICPerturberEffect.randomize: 2>
set = <GenKICPerturberEffect.set: 1>
class pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber

Bases: pybind11_builtins.pybind11_object

add_atom_set(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, atomset: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) None
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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::add_atom_set(const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

add_inputvalue(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, inputvalue: float) None

Adds a real value to the list of real input values.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::add_inputvalue(const double &) –> void

add_residue(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, residue_index: int) None

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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::add_residue(const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, 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) None

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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::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> > > > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

assign(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, : pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::operator=(const class protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber &) –> class protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber &

attach_boinc_ghost_observer(self: pyrosetta.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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::attach_boinc_ghost_observer() const –> bool

bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) str

Get the bin that the set_backbone_bin perturber will use.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::bin() const –> std::string

clear_residues(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) None

Clears the residue list for this perturber

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::clear_residues() –> void

clone(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::clone() const –> class std::shared_ptr<class protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber>

custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) pyrosetta.rosetta.core.scoring.Rama_Table_Type

Get the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::custom_rama_table() const –> enum core::scoring::Rama_Table_Type

static define_valid_perturber_name_enumeration(xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::define_valid_perturber_name_enumeration(class utility::tag::XMLSchemaDefinition &) –> void

get_name(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) str

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_name() const –> std::string

get_perturber_effect(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect

Returns the enum type for the effect of this perturber.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_perturber_effect() const –> enum protocols::generalized_kinematic_closure::perturber::perturber_effect

static get_perturber_effect_from_name(name: str) pyrosetta.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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_perturber_effect_from_name(const std::string &) –> enum protocols::generalized_kinematic_closure::perturber::perturber_effect

static get_perturber_effect_name(effect: int) str
Returns the name of a perturber given the enum type.

Returns “unknown_effect” if no such effect exists.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::get_perturber_effect_name(unsigned long &) –> std::string

init_bbgmover(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, loop_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) None

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::init_bbgmover(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> > > &) –> void

iterations(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber) int

Return the number of iterations for this perturber

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::iterations() const –> unsigned long

load_bin_params(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, bin_params_file: str) None

Initializes the BinTransitionCalculator object and loads a bin_params file.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::load_bin_params(const std::string &) –> void

must_switch_bins(self: pyrosetta.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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::must_switch_bins() const –> bool

set_attach_boinc_ghost_observer(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, 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::perturber::GeneralizedKICperturber::set_attach_boinc_ghost_observer(const bool) –> void

set_bin(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, bin: str) None

Set the bin that the set_backbone_bin perturber will use.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_bin(const std::string &) –> void

set_custom_rama_table(*args, **kwargs)

Overloaded function.

  1. set_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, type: pyrosetta.rosetta.core.scoring.Rama_Table_Type) -> None

Set the custom Ramachandran table (by enum) for the perturb_alpha_backbone_by_rama perturber.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_custom_rama_table(const enum core::scoring::Rama_Table_Type) –> void

  1. set_custom_rama_table(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, name: str) -> None

Set the custom Ramachandran table (by name) for the perturb_alpha_backbone_by_rama perturber.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_custom_rama_table(const std::string &) –> void

set_iterations(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, val: int) None

Set the number of iterations for this perturber

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_iterations(const unsigned long) –> void

set_must_switch_bins(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, val: bool) None
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.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_must_switch_bins(const bool) –> void

set_perturber_effect(*args, **kwargs)

Overloaded function.

  1. set_perturber_effect(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, effect: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect) -> None

Sets the effect of this perturber.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_perturber_effect(const enum protocols::generalized_kinematic_closure::perturber::perturber_effect &) –> void

  1. set_perturber_effect(self: pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.GeneralizedKICperturber, effectname: str) -> None

Sets the effect of this perturber using the perturber effect name.

Exits with an error message if the name is unknown.

C++: protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::set_perturber_effect(const std::string &) –> void

class pyrosetta.rosetta.protocols.generalized_kinematic_closure.perturber.perturber_effect

Bases: pybind11_builtins.pybind11_object

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.

Members:

no_effect

set_dihedral

set_bondangle

set_bondlength

set_backbone_bin

randomize_dihedral

randomize_alpha_backbone_by_rama

randomize_backbone_by_rama_prepro

randomize_backbone_by_bins

perturb_bondlength

perturb_bondangle

perturb_dihedral

perturb_dihedral_bbg

perturb_backbone_by_bins

copy_backbone_dihedrals

mirror_backbone_dihedrals

sample_cis_peptide_bond

unknown_effect

end_of_effect_list

copy_backbone_dihedrals = <perturber_effect.copy_backbone_dihedrals: 15>
end_of_effect_list = <perturber_effect.unknown_effect: 18>
mirror_backbone_dihedrals = <perturber_effect.mirror_backbone_dihedrals: 16>
property name
no_effect = <perturber_effect.no_effect: 1>
perturb_backbone_by_bins = <perturber_effect.perturb_backbone_by_bins: 14>
perturb_bondangle = <perturber_effect.perturb_bondangle: 11>
perturb_bondlength = <perturber_effect.perturb_bondlength: 10>
perturb_dihedral = <perturber_effect.perturb_dihedral: 12>
perturb_dihedral_bbg = <perturber_effect.perturb_dihedral_bbg: 13>
randomize_alpha_backbone_by_rama = <perturber_effect.randomize_alpha_backbone_by_rama: 7>
randomize_backbone_by_bins = <perturber_effect.randomize_backbone_by_bins: 9>
randomize_backbone_by_rama_prepro = <perturber_effect.randomize_backbone_by_rama_prepro: 8>
randomize_dihedral = <perturber_effect.randomize_dihedral: 6>
sample_cis_peptide_bond = <perturber_effect.sample_cis_peptide_bond: 17>
set_backbone_bin = <perturber_effect.set_backbone_bin: 5>
set_bondangle = <perturber_effect.set_bondangle: 3>
set_bondlength = <perturber_effect.set_bondlength: 4>
set_dihedral = <perturber_effect.set_dihedral: 2>
unknown_effect = <perturber_effect.unknown_effect: 18>