helical_bundle¶

parameters

Bindings for protocols::helical_bundle namespace

class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper¶

Bases: pybind11_builtins.pybind11_object

BackboneGridSamplerHelper class, which stores options for the PerturbBundle mover.

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, : pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper¶: C++: protocols::helical_bundle::BackboneGridSamplerHelper::operator=(const class protocols::helical_bundle::BackboneGridSamplerHelper &) –> class protocols::helical_bundle::BackboneGridSamplerHelper &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper¶

Copy this BackboneGridSamplerHelper object( allocate actual memory for it )

C++: protocols::helical_bundle::BackboneGridSamplerHelper::clone() const –> class std::shared_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper¶: C++: protocols::helical_bundle::BackboneGridSamplerHelper::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BackboneGridSamplerHelper_t¶: C++: protocols::helical_bundle::BackboneGridSamplerHelper::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::BackboneGridSamplerHelper>

increment_cur_indices(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → None¶

RECURSIVE function that increments the current sample index.

This function adds 1 to the last torsion index. If the last torsion index value exceeds the number of samples for that torsion, it resets that torsion index and increments the second-last torsion index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::increment_cur_indices() –> void

n_torsions(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, res_index: int) → int¶

Returns the number of different mainchain torsions that the BackboneGridSampler will sample over.

Returns a value for the residue in the repeating unit with index res_index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions(const unsigned long) const –> unsigned long

n_torsions_total(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → int¶

Returns the total number of mainchain torsions over which we will sample.

This is the sum of the n_torsions_ entries for each residue in the repeating

unit, and is initialized by the initialize_samples() function.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::n_torsions_total() const –> unsigned long

reset(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → None¶

Reset this BackboneGridSamplerHelper object.

Clears all internal data.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::reset() –> void

residue_index(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → int¶

Returns the residue index in the repeating unit (1st, 2nd, 3rd etc.) corresponding to a: given torsion index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::residue_index(const unsigned long) const –> unsigned long

residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper) → int¶

Returns the number of residues per repeat, set by the initialize_data() function.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::residues_per_repeat() const –> unsigned long

torsion_id(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → int¶

Returns the torsion ID for the specified torsion index.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::torsion_id(const unsigned long) const –> unsigned long

torsion_sample_value(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, index: int) → float¶

Returns the current sample value for the specified torsion.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::torsion_sample_value(const unsigned long &) const –> double

class pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper¶

Bases: pybind11_builtins.pybind11_object

BundleGridSamplerHelper class, which stores options for the PerturbBundle mover.

DoF_helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → int¶

Returns the helix index of the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_helix_index(const unsigned long &) const –> unsigned long

DoF_name(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, type: pyrosetta.rosetta.protocols.helical_bundle.DoFType) → str¶

Return the name of a DoF type given its enum.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_name(const enum protocols::helical_bundle::DoFType &) const –> std::string

DoF_sample_value(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → float¶

Returns the current sample value for the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_sample_value(const unsigned long &) const –> double

DoF_type(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, index: int) → pyrosetta.rosetta.protocols.helical_bundle.DoFType¶

Returns the DoF type of the specified DoF.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_type(const unsigned long &) const –> enum protocols::helical_bundle::DoFType

add_DoF(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, doftype: pyrosetta.rosetta.protocols.helical_bundle.DoFType, helix_index: int, n_samples: int, lower_val: float, upper_val: float) → None¶

Add an allowed DoF that the BundleGridSampler will sample over.

Must specify the DoF type, the helix index, the number of samples, and the lower and upper bounds of the range to be sampled.

C++: protocols::helical_bundle::BundleGridSamplerHelper::add_DoF(const enum protocols::helical_bundle::DoFType, const unsigned long, const unsigned long, const double &, const double &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, : pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper¶: C++: protocols::helical_bundle::BundleGridSamplerHelper::operator=(const class protocols::helical_bundle::BundleGridSamplerHelper &) –> class protocols::helical_bundle::BundleGridSamplerHelper &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper¶

Copy this BundleGridSamplerHelper object( allocate actual memory for it )

C++: protocols::helical_bundle::BundleGridSamplerHelper::clone() const –> class std::shared_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper¶: C++: protocols::helical_bundle::BundleGridSamplerHelper::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_BundleGridSamplerHelper_t¶: C++: protocols::helical_bundle::BundleGridSamplerHelper::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::BundleGridSamplerHelper>

increment_cur_indices(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None¶

RECURSIVE function that increments the current sample index.

This function adds 1 to the last DoF index. If the last DoF index value exceeds the number of samples for that DoF, it resets that DoF index and increments the second-last DoF index by 1 by recursively calling itself. This function is overloaded; the public version by default tries to increment the last index, while the private version can be called recursively.

C++: protocols::helical_bundle::BundleGridSamplerHelper::increment_cur_indices() –> void

initialize_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None¶

Perform the pre-calculation that sets up the lists of parameter values to be sampled.

C++: protocols::helical_bundle::BundleGridSamplerHelper::initialize_samples() –> void

nDoFs(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → int¶

Returns the number of different DoFs that the BundleGridSampler will sample over.

C++: protocols::helical_bundle::BundleGridSamplerHelper::nDoFs() const –> unsigned long

reset(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper) → None¶

Reset this BundleGridSamplerHelper object.

Clears all internal data.

C++: protocols::helical_bundle::BundleGridSamplerHelper::reset() –> void

class pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour¶

Bases: pybind11_builtins.pybind11_object

The behaviour of this filter.

The filter can return true always, false always, or can filter by energy. If you update this enum, add new behaviours to the two set_filter_behaviour() functions (setting by string and by enum).

Members:

brf_always_true

brf_always_false

brf_filter_by_energy

brf_undefined

class pyrosetta.rosetta.protocols.helical_bundle.DoFType¶

Bases: pybind11_builtins.pybind11_object

The type of bundle parameter that will be sampled by the: BundleGridSampler mover.

Members:

bgsh_r0

bgsh_omega0

bgsh_delta_omega0

bgsh_delta_omega1

bgsh_delta_t

bgsh_z1_offset

bgsh_z0_offset

bgsh_epsilon

bgsh_undefined_dof

class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc¶

Bases: pyrosetta.rosetta.core.optimization.Multifunc

Multifunction class for fitting a simple (straight) helix to the Crick parameters.

abort_min(self: pyrosetta.rosetta.core.optimization.Multifunc, : pyrosetta.rosetta.utility.vector1_double) → bool¶

Christophe added the following to allow premature end of minimization: If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN!

C++: core::optimization::Multifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

assign(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, : pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc) → pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc¶: C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::operator=(const class protocols::helical_bundle::FitSimpleHelixMultiFunc &) –> class protocols::helical_bundle::FitSimpleHelixMultiFunc &

dfunc(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None¶

Calculate function value derivatives

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc, vars: pyrosetta.rosetta.utility.vector1_double, vars2: pyrosetta.rosetta.utility.vector1_double) → None¶

Error state reached – derivative does not match gradient

C++: protocols::helical_bundle::FitSimpleHelixMultiFunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.PertType¶

Bases: pybind11_builtins.pybind11_object

The type of random perturbation that will be used.

Members:

pt_uniform

pt_gaussian

pt_undefined_perturbation

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions¶

Bases: pybind11_builtins.pybind11_object

PerturbBundleOptions class, which stores options for the PerturbBundle mover.

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions¶: C++: protocols::helical_bundle::PerturbBundleOptions::operator=(const class protocols::helical_bundle::PerturbBundleOptions &) –> class protocols::helical_bundle::PerturbBundleOptions &

clone(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions¶

Copy this residue( allocate actual memory for it )

C++: protocols::helical_bundle::PerturbBundleOptions::clone() const –> class std::shared_ptr<class protocols::helical_bundle::PerturbBundleOptions>

default_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float¶

Returns the default value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::default_value() const –> double

delta(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float¶

Function to generate a random value, based on the perturbation type and perturbation magnitude.

Typically, one would then add this value to the current parameter value to perturb it.

C++: protocols::helical_bundle::PerturbBundleOptions::delta() const –> double

get_self_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions¶: C++: protocols::helical_bundle::PerturbBundleOptions::get_self_ptr() –> class std::shared_ptr<class protocols::helical_bundle::PerturbBundleOptions>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.std.weak_ptr_protocols_helical_bundle_PerturbBundleOptions_t¶: C++: protocols::helical_bundle::PerturbBundleOptions::get_self_weak_ptr() –> class std::weak_ptr<class protocols::helical_bundle::PerturbBundleOptions>

helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int¶

Returns the index of the helix that these options refer to.

C++: protocols::helical_bundle::PerturbBundleOptions::helix_index() const –> unsigned long

is_being_set(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool¶

Returns whether this parameter is being set to its default value.

Used by the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::is_being_set() const –> bool

is_copy(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool¶

Returns whether we’re copying this value from another helix.

C++: protocols::helical_bundle::PerturbBundleOptions::is_copy() const –> bool

is_perturbable(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool¶

Returns whether this option is set to be peturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::is_perturbable() const –> bool

lower_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float¶

Returns the lower sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::lower_value() const –> double

omega0_copies_pitch_instead(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool¶

Special case: returns whether omega0 copying should use the pitch angle instead of the omega0 value.

Default false.

C++: protocols::helical_bundle::PerturbBundleOptions::omega0_copies_pitch_instead() const –> bool

other_helix(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int¶

Returns the other helix index from which we’re copying a value.

C++: protocols::helical_bundle::PerturbBundleOptions::other_helix() const –> unsigned long

perturbation_magnitude(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float¶

Returns the perturbation magnitude. Returns 0 if not perturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::perturbation_magnitude() const –> double

perturbation_type(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → pyrosetta.rosetta.protocols.helical_bundle.PertType¶

Returns the perturbation type.

C++: protocols::helical_bundle::PerturbBundleOptions::perturbation_type() const –> enum protocols::helical_bundle::PertType

samples(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → int¶

Returns the number of values to sample for this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If the sample value is 0, no sampling occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::samples() const –> unsigned long

set_being_set(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None¶

Sets whether this parameter is being set to its default value.

Used by the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_being_set(const bool) –> void

set_default_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None¶

Set the default value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_default_value(const double &) –> void

set_helix_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: int) → None¶

Sets the index of the helix that these options refer to.

C++: protocols::helical_bundle::PerturbBundleOptions::set_helix_index(const unsigned long) –> void

set_helix_to_copy(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, helix_index: int) → None¶

Sets the helix from which we should copy a parameter value. If set to zero, no copying occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::set_helix_to_copy(const unsigned long) –> void

set_lower_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None¶

Set the lower sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_lower_value(const double &) –> void

set_omega0_copies_pitch_instead(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, copy_pitch: bool) → None¶

Special case: sets whether omega0 copying should copy the pitch angle instead of the omega0 value.

C++: protocols::helical_bundle::PerturbBundleOptions::set_omega0_copies_pitch_instead(const bool) –> void

set_perturbable(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None¶

Sets whether this option is peturbable.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbable(const bool) –> void

set_perturbation_magnitude(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None¶

Sets the perturbation magnitude. Sets perturbable to true in the process.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbation_magnitude(const double &) –> void

set_perturbation_type(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, type: pyrosetta.rosetta.protocols.helical_bundle.PertType) → None¶

Sets the perturbation type.

C++: protocols::helical_bundle::PerturbBundleOptions::set_perturbation_type(const enum protocols::helical_bundle::PertType) –> void

set_samples(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: int) → None¶

Sets the number of values to sample for this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover. If set to 0, no sampling occurs.

C++: protocols::helical_bundle::PerturbBundleOptions::set_samples(const unsigned long) –> void

set_upper_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: float) → None¶

Set the upper sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::set_upper_value(const double &) –> void

set_use_defaults(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions, val: bool) → None¶

Sets whether the default values should be used in lieu of whatever is set here.

C++: protocols::helical_bundle::PerturbBundleOptions::set_use_defaults(const bool) –> void

upper_value(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → float¶

Returns the upper sampled value of this parameter.

This is used by the BundleGridSampler mover, but not the PerturbBundle mover.

C++: protocols::helical_bundle::PerturbBundleOptions::upper_value() const –> double

use_defaults(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleOptions) → bool¶

Returns whether the default values should be used in lieu of whatever is set here.

C++: protocols::helical_bundle::PerturbBundleOptions::use_defaults() const –> bool

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_dofs(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_make_bundle_dofs(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_minorhelix_defaults(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_make_bundle_minorhelix_defaults(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_other_defaults(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_make_bundle_other_defaults(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_make_bundle_symmetry(attlist: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_make_bundle_symmetry(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_minor_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_minor_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.add_attributes_for_other_helix_params(subtag_attributes: pyrosetta.rosetta.std.list_utility_tag_XMLSchemaAttribute_t) → None¶: C++: protocols::helical_bundle::add_attributes_for_other_helix_params(class std::list<class utility::tag::XMLSchemaAttribute, class std::allocator<class utility::tag::XMLSchemaAttribute> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.align_mainchain_atoms(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None¶

Align mainchain atoms of pose to ref_pose mainchain atoms.

C++: protocols::helical_bundle::align_mainchain_atoms(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.align_mainchain_atoms_of_residue_range(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None¶

Align mainchain atoms of pose to ref_pose mainchain atoms,: moving ONLY the residues involved in the alignment.

C++: protocols::helical_bundle::align_mainchain_atoms_of_residue_range(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_bondangles(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None¶

Copy backbone bond angle values from one pose, where helix mainchain atom coordinates have been: set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_bondangles(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_bondlengths(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None¶

Copy backbone bond length values from one pose, where helix mainchain atom coordinates have been: set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_bondlengths(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.copy_helix_dihedrals(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) → None¶

Copy backbone dihedral values from one pose, where helix mainchain atom coordinates have been: set with the Crick equations, to another with ideal geometry.

C++: protocols::helical_bundle::copy_helix_dihedrals(class core::pose::Pose &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.generate_atom_positions(outvector: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, helixpose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int, r0: float, omega0: float, delta_omega0: float, delta_t: float, z1_offset: float, z0_offset: float, epsilon: float, invert_helix: bool, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_omega1_all: float, delta_z1: pyrosetta.rosetta.utility.vector1_double, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long, repeating_unit_offset: int, failed: bool) → None¶

Generate the x,y,z coordinates of the mainchain atoms using the Crick equations.

Coordinates will be returned as a vector of vectors of xyzVectors. The outer index will refer to residue number, and the inner index will refer to atom number. Returns failed=true if coordinates could not be generated, false otherwise.

C++: protocols::helical_bundle::generate_atom_positions(class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, const class core::pose::Pose &, const unsigned long, const unsigned long, const double &, const double &, const double &, const double &, const double &, const double &, const double &, const bool, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const unsigned long, bool &) –> void

pyrosetta.rosetta.protocols.helical_bundle.parse_resnames(string_in: str, vect_out: pyrosetta.rosetta.utility.vector1_std_string) → None¶

Given a comma-separated list of residue names, separate these out into a vector of

residue names.

The string_in string is the input; the vect_out vector is the output (which will be reset by this operation).

C++: protocols::helical_bundle::parse_resnames(const class std::basic_string<char> &, class utility::vector1<class std::basic_string<char>, class std::allocator<class std::basic_string<char> > > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.place_atom_positions(pose: pyrosetta.rosetta.core.pose.Pose, atom_positions: pyrosetta.rosetta.utility.vector1_utility_vector1_numeric_xyzVector_double_std_allocator_numeric_xyzVector_double_t, helix_start: int, helix_end: int) → None¶

Place the helix mainchain atoms based on the Crick equations.

C++: protocols::helical_bundle::place_atom_positions(class core::pose::Pose &, const class utility::vector1<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > >, class std::allocator<class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > > > &, const unsigned long, const unsigned long) –> void

pyrosetta.rosetta.protocols.helical_bundle.read_minor_helix_params(filename: str, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long) → None¶

Read minor helix parameters from a crick_params file.

C++: protocols::helical_bundle::read_minor_helix_params(const class std::basic_string<char> &, class utility::vector1<double, class std::allocator<double> > &, double &, double &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &, unsigned long &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.write_crick_params_file_data(outfile: pyrosetta.rosetta.utility.io.ozstream, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) → None¶

Actual write of the crick_params file data.

Called by both write_minor_helix_params variants. The outfile ozstream must already be opened, and will not be closed by this function.

C++: protocols::helical_bundle::write_crick_params_file_data(class utility::io::ozstream &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.protocols.helical_bundle.write_minor_helix_params(*args, **kwargs)¶

Overloaded function.

write_minor_helix_params(filename: str, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) -> None

Write out a crick_params file.

Variant for case of a single-residue repeating unit.

C++: protocols::helical_bundle::write_minor_helix_params(const class std::basic_string<char> &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

write_minor_helix_params(filename: str, residues_per_repeat: int, atoms_per_residue: pyrosetta.rosetta.utility.vector1_unsigned_long, r1: pyrosetta.rosetta.utility.vector1_double, omega1: float, z1: float, delta_omega1: pyrosetta.rosetta.utility.vector1_double, delta_z1: pyrosetta.rosetta.utility.vector1_double) -> None

Write out a crick_params file.

Variant for case of a multi-residue repeating unit.

C++: protocols::helical_bundle::write_minor_helix_params(const class std::basic_string<char> &, const unsigned long &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<double, class std::allocator<double> > &, const double &, const double &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void