helical_bundle_predict

Bindings for protocols::helical_bundle_predict namespace

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix

Bases: pybind11_object

An individual helix. This class stores start and end positions, plus helical parameters.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix

C++: protocols::helical_bundle_predict::HBPHelix::operator=(const class protocols::helical_bundle_predict::HBPHelix &) –> class protocols::helical_bundle_predict::HBPHelix &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix

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

C++: protocols::helical_bundle_predict::HBPHelix::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBPHelix>

crick_params_filename(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → str

Get the filename for the Crick params for this helix.

Used to determine whether two helices are of a matching type.

C++: protocols::helical_bundle_predict::HBPHelix::crick_params_filename() const –> const std::string &

determine_repeating_unit_offset(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, pose: pyrosetta.rosetta.core.pose.Pose, start_position: int, end_position: int) → int

Given the start and end position of a helix, determine from the residue composition what the repeating unit offset should be.

For example, if the stretch had pattern alpha-alpha-beta-alpha, and the Crick params file expected alpha-alpha-alpha-beta, the offset would be 3.

C++: protocols::helical_bundle_predict::HBPHelix::determine_repeating_unit_offset(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> unsigned long

end_position(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → int

Get the end position.

C++: protocols::helical_bundle_predict::HBPHelix::end_position() const –> unsigned long

extension_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → float

Get the probability of extending an existing helix.

C++: protocols::helical_bundle_predict::HBPHelix::extension_prob() const –> const double &

is_in_helix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, seqpos: int) → bool

Is a sequence position within a helix?

Returns false if either of startpos or endpos is zero.

C++: protocols::helical_bundle_predict::HBPHelix::is_in_helix(const unsigned long) const –> bool

nucleation_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → float

Get the probability of nucleating a helix.

C++: protocols::helical_bundle_predict::HBPHelix::nucleation_prob() const –> const double &

parameters(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters

Get the parameters (nonconst access).

C++: protocols::helical_bundle_predict::HBPHelix::parameters() –> class std::shared_ptr<class protocols::helical_bundle_predict::HBPHelixParameters>

residues_per_turn(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → int

Get the number of residues per turn of this helix type.

C++: protocols::helical_bundle_predict::HBPHelix::residues_per_turn() const –> unsigned long

retraction_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → float

Get the probability of shrinking an existing helix.

C++: protocols::helical_bundle_predict::HBPHelix::retraction_prob() const –> const double &

set_crick_params_filename(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, name_in: str) → None

Set the filename for the Crick params for this helix.

Used to determine whether two helices are of a matching type.

C++: protocols::helical_bundle_predict::HBPHelix::set_crick_params_filename(const std::string &) –> void

set_end_position(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, position_in: int) → None

Set the end position.

C++: protocols::helical_bundle_predict::HBPHelix::set_end_position(const unsigned long) –> void

set_extension_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, setting: float) → None

Set the probability of extending an existing helix.

C++: protocols::helical_bundle_predict::HBPHelix::set_extension_prob(const double &) –> void

set_nucleation_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, setting: float) → None

Set the probability of nucleating a helix.

C++: protocols::helical_bundle_predict::HBPHelix::set_nucleation_prob(const double &) –> void

set_retraction_prob(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, setting: float) → None

Set the probability of shrinking an existing helix.

C++: protocols::helical_bundle_predict::HBPHelix::set_retraction_prob(const double &) –> void

set_start_position(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix, position_in: int) → None

Set the start position.

C++: protocols::helical_bundle_predict::HBPHelix::set_start_position(const unsigned long) –> void

start_position(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelix) → int

Get the start position.

C++: protocols::helical_bundle_predict::HBPHelix::start_position() const –> unsigned long

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments

Bases: pybind11_object

A class for storing the helix assignments for a pose. This can represent those proposed from an input file, or those at the current state of a trajectory.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, src: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments

Assignment operator.

Deep-clones helices.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::operator=(const class protocols::helical_bundle_predict::HBPHelixAssignments &) –> class protocols::helical_bundle_predict::HBPHelixAssignments &

clear(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → None

Reset this object.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::clear() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments

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

C++: protocols::helical_bundle_predict::HBPHelixAssignments::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBPHelixAssignments>

confine_to_user_defined_helices(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Are we supposed to keep sampled helices within the user-defined ranges?

C++: protocols::helical_bundle_predict::HBPHelixAssignments::confine_to_user_defined_helices() const –> bool

get_containing_helix_index(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, seqpos: int) → int

Given a sequence position, get the helix index that contains it.

Returns zero if no helix contains this sequence position.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::get_containing_helix_index(const unsigned long) const –> unsigned long

initialize_from_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, file_contents: str) → None

Set this object up from the contents of a file.

Warning! Reads Crick params files from disk!

C++: protocols::helical_bundle_predict::HBPHelixAssignments::initialize_from_file_contents(const std::string &) –> void

initialize_from_psipred_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, psipred_file_contents: str, helix_prob_cutoff: float, strand_prob_cutoff: float) → None

Set this object up from the contents of a PsiPred prediction file.

Warning! Reads Crick params files from disk!

This can only set up left-handed alpha helix and beta strand secondary structures. Globals must be set by a prior call to HBPHelixAssignments::initialize_from_file_contents().

C++: protocols::helical_bundle_predict::HBPHelixAssignments::initialize_from_psipred_file_contents(const std::string &, const double, const double) –> void

is_in_helix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, sequence_index: int) → bool

Given a sequence index, determine whether it is in a helix.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::is_in_helix(const unsigned long) const –> bool

try_elongating_helix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose, reference_helix_assignments: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Roll a die and decide whether to elongate a helix at the present position.

If we do it, then we add one residue to the helix (updating the helices_ list). The probabilities for elongation are taken from the adjacent helix.

Does nothing if the present position is not adjacent to a helix. Automatically merges helices if the present position bridges two helices, and we decide to elongate. In this case, the parameters of one helix are randomly chosen as the parameters to keep.

True if we elongated here, false otherwise.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::try_elongating_helix(const unsigned long, const class core::pose::Pose &, const class protocols::helical_bundle_predict::HBPHelixAssignments &) –> bool

try_nucleating_helix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose, reference_helix_assignments: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Roll a die and decide whether to nucleate a helix at the present position.

If we do it, then we add one turn of helix as a new helix (updating the helices_ list), and we copy helix parameters from reference_helix_assignments. The probabilities for nucleation are taken from reference_helix_assignments.

Automatically merges helices if the set of residues in question overlaps with another helix. In this case, the parameters of the other helix are chosen as the parameters to keep.

True if we nucleated here, false otherwise.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::try_nucleating_helix(const unsigned long, const class core::pose::Pose &, const class protocols::helical_bundle_predict::HBPHelixAssignments &) –> bool

try_perturbing_global_helix_parameters(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Try perturbing the parameters for all helices.

Updates individual helices if parameters are perturbed.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::try_perturbing_global_helix_parameters() –> bool

try_perturbing_local_helix_parameters(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Try perturbing the parameters of individual helices, that are not set to copy globals.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::try_perturbing_local_helix_parameters() –> bool

try_retracting_helix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments, seqpos: int, pose: pyrosetta.rosetta.core.pose.Pose, reference_helix_assignments: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixAssignments) → bool

Roll a die and decide whether to contract a helix at the present position.

If we do it, then we subtract one residue from the helix (updating the helices_ list). The probabilities for retraction are taken from the adjacent helix. If the helix shrinks to zero size, then we remove it from the helices_ list.

Does nothing if the present position is not at one of the ends of a helix.

True if we retracted here, false otherwise.

C++: protocols::helical_bundle_predict::HBPHelixAssignments::try_retracting_helix(const unsigned long, const class core::pose::Pose &, const class protocols::helical_bundle_predict::HBPHelixAssignments &) –> bool

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters

Bases: pybind11_object

Helical parameters stored by the HBPHelix class.

Allows the HBPHelix class to avoid storing these parameters if it needn’t.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters

C++: protocols::helical_bundle_predict::HBPHelixParameters::operator=(const class protocols::helical_bundle_predict::HBPHelixParameters &) –> class protocols::helical_bundle_predict::HBPHelixParameters &

bundle_calculator(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Access the bundle calculator (nonconst-access).

C++: protocols::helical_bundle_predict::HBPHelixParameters::bundle_calculator() –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters

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

C++: protocols::helical_bundle_predict::HBPHelixParameters::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBPHelixParameters>

create_calculator_from_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, filename: str) → None

Create a new bundle parameterization calculator, and initialize it from a Crick params file.

WARNING! Triggers read from disk!

C++: protocols::helical_bundle_predict::HBPHelixParameters::create_calculator_from_file(const std::string &) –> void

delta_omega1_range(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → Tuple[float, float]

Get the delta_omega1 range.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::delta_omega1_range() const –> const struct std::pair<double, double> &

omega0_range(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → Tuple[float, float]

Get the omega0 range.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::omega0_range() const –> const struct std::pair<double, double> &

r0_range(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters) → Tuple[float, float]

Get the r0 range.

C++: protocols::helical_bundle_predict::HBPHelixParameters::r0_range() const –> const struct std::pair<double, double> &

set_calculator(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, calculator_in: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) → None

Set the bundle parameterization calculator.

Input is cloned.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_calculator(const class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator> &) –> void

set_delta_omega1_max(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set maximum delta_omega1 value.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_delta_omega1_max(const double &) –> void

set_delta_omega1_min(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set minimum delta_omega1 value.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_delta_omega1_min(const double &) –> void

set_omega0_max(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set maximum omega0 value.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_omega0_max(const double &) –> void

set_omega0_min(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set minimum omega0 value.

Settings should be in radians.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_omega0_min(const double &) –> void

set_r0_max(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set maximum r0 value.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_r0_max(const double &) –> void

set_r0_min(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBPHelixParameters, setting: float) → None

Set minimum r0 value.

C++: protocols::helical_bundle_predict::HBPHelixParameters::set_r0_min(const double &) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator

Bases: HBP_MoveGenerator

A class to generate ParsedProtocols for the final full-atom refinement step.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator

C++: protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator::operator=(const class protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator &) –> class protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Clone this object: that is, make a copy and return an owning pointer to the copy.

C++: protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_MoveGenerator>

current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::current_round() const –> unsigned long

generate_monte_carlo_move(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_FinalFullatomRefinementMoveGenerator, current_step: int, num_steps: int, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::rosetta_scripts::ParsedProtocol

Given the current step index, the total number of steps in the trajectory, and the pose for analysis,

construct a ParsedProtocol of things to do to this pose for this move in the Monte Carlo trajectory.

Pure virtual. Must be implemented by derived classes.

C++: protocols::helical_bundle_predict::HBP_FinalFullatomRefinementMoveGenerator::generate_monte_carlo_move(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

mark_move_accepted(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → None

Does nothing in base class. Can be overridden in derived classes to do something

more useful when a move is accepted.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::mark_move_accepted() const –> void

mark_move_rejected(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → None

Does nothing in base class. Can be overridden in derived classes to do something

more useful when a move is rejected.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::mark_move_rejected() const –> void

max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the maximum number of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::max_rounds() const –> unsigned long

set_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_current_round(const unsigned long) –> void

set_max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the total nunmber of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_max_rounds(const unsigned long) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator

Bases: HBP_MoveGenerator

A class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose. This version uses helix-coil transition theory to nucleate and extend helices.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::operator=(const class protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator &) –> class protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Clone this object: that is, make a copy and return an owning pointer to the copy.

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_MoveGenerator>

current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::current_round() const –> unsigned long

generate_monte_carlo_move(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator, current_step: int, num_steps: int, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::rosetta_scripts::ParsedProtocol

Given the current step index, the total number of steps in the trajectory, and the pose for analysis,

construct a ParsedProtocol of things to do to this pose for this move in the Monte Carlo trajectory.

This override uses helix-coil transition theory to nucleate, extend, or remove helix segments. Non-helix segments are simply subjected to small moves.

A ParsedProtocolOP with the new protocol for success, or nullptr for failure.

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::generate_monte_carlo_move(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

mark_move_accepted(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator) → None

When a move is accepted, set the current helix assignments to the candidate helix assignments.

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::mark_move_accepted() const –> void

mark_move_rejected(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → None

Does nothing in base class. Can be overridden in derived classes to do something

more useful when a move is rejected.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::mark_move_rejected() const –> void

max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the maximum number of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::max_rounds() const –> unsigned long

set_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_current_round(const unsigned long) –> void

set_max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the total nunmber of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_max_rounds(const unsigned long) –> void

set_up_user_helix_assignments(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator, file_contents: str) → None

Given a helix assignment file’s contents, set up the helix assignments.

Involves no read from disk.

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::set_up_user_helix_assignments(const std::string &) –> void

set_up_user_helix_assignments_from_psipred_predictions(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_HelixCoilMoveGenerator, psipred_file_contents: str, helix_prob_cutoff: float, strand_prob_cutoff: float) → None

Given PsiPred predictions, set up the helix assignments.

Can only set up left-handed alpha helix and beta strand predictions, of course.

Involves no read from disk.

C++: protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::set_up_user_helix_assignments_from_psipred_predictions(const std::string &, const double, const double) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Bases: pybind11_object

A base class for a module to generate ParsedProtocols for the next move in a Monte Carlo trajectory, based on the current state of the pose.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::operator=(const class protocols::helical_bundle_predict::HBP_MoveGenerator &) –> class protocols::helical_bundle_predict::HBP_MoveGenerator &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Clone this object: that is, make a copy and return an owning pointer to the copy.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_MoveGenerator>

current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::current_round() const –> unsigned long

generate_monte_carlo_move(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, current_step: int, num_steps: int, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::rosetta_scripts::ParsedProtocol

Given the current step index, the total number of steps in the trajectory, and the pose for analysis,

construct a ParsedProtocol of things to do to this pose for this move in the Monte Carlo trajectory.

Pure virtual. Must be implemented by derived classes.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::generate_monte_carlo_move(const unsigned long, const unsigned long, const class core::pose::Pose &) const –> class std::shared_ptr<class protocols::rosetta_scripts::ParsedProtocol>

mark_move_accepted(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → None

Does nothing in base class. Can be overridden in derived classes to do something

more useful when a move is accepted.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::mark_move_accepted() const –> void

mark_move_rejected(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → None

Does nothing in base class. Can be overridden in derived classes to do something

more useful when a move is rejected.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::mark_move_rejected() const –> void

max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator) → int

Get the maximum number of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::max_rounds() const –> unsigned long

set_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the current round.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_current_round(const unsigned long) –> void

set_max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator, setting: int) → None

Set the total nunmber of rounds.

C++: protocols::helical_bundle_predict::HBP_MoveGenerator::set_max_rounds(const unsigned long) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator

Bases: HBP_TemperatureScheduleGenerator

A class to generate a temperature ramping scheme for a simulated annealing trajectory. This version ramps sigmoidally.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator

C++: protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::operator=(const class protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator &) –> class protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator &

calculate_current_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator, current_step: int, max_steps: int) → float

Calculate the current temperature for this point in the trajectory.

C++: protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::calculate_current_temperature(const unsigned long, const unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator

Copy this object and return an owning pointe to the copy.

C++: protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator>

current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → int

Get the index of the current round of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::current_round() const –> unsigned long

get_max_temp_for_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature, given the round.

Round must be set, and greater than zero. The base class version of this function just returns max_temperature_, but this can be overridden if a derived class wants to do something more complicated.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::get_max_temp_for_current_round() const –> double

get_min_temp_for_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the minimum temperature, given the round.

Round must be set, and greater than zero. The base class version of this function just returns min_temperature_, but this can be overridden if a derived class wants to do something more complicated.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::get_min_temp_for_current_round() const –> double

max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → int

Get the total nunmber of rounds of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::max_rounds() const –> unsigned long

max_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::max_temperature() const –> const double &

min_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::min_temperature() const –> const double &

set_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, setting: int) → None

Set the index of the current round of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_current_round(const unsigned long) –> void

set_exponent(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_SigmoidalTemperatureScheduleGenerator, setting: float) → None

Set the exponent.

This is a value that determines how S-shaped the sigmoid is. A value of 1 gives a straight line; higher values have more lag at start and end.

Must be greater than zero.

C++: protocols::helical_bundle_predict::HBP_SigmoidalTemperatureScheduleGenerator::set_exponent(const double &) –> void

set_max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, setting: int) → None

Set the total nunmber of rounds of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_max_rounds(const unsigned long) –> void

set_max_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, temp_in: float) → None

Set the maximum temperature for the run.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_max_temperature(const double &) –> void

set_min_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, temp_in: float) → None

Set the minimum temperature for the run.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_min_temperature(const double &) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator

Bases: pybind11_object

A base class to generate a temperature ramping scheme for a simulated annealing trajectory.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, : pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::operator=(const class protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator &) –> class protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator &

calculate_current_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, current_step: int, max_steps: int) → float

Calculate the current temperature for this point in the trajectory.

Pure virtual. Must be implemented by derived classes.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::calculate_current_temperature(const unsigned long, const unsigned long) const –> double

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator

Copy this object and return an owning pointe to the copy.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator>

current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → int

Get the index of the current round of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::current_round() const –> unsigned long

get_max_temp_for_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature, given the round.

Round must be set, and greater than zero. The base class version of this function just returns max_temperature_, but this can be overridden if a derived class wants to do something more complicated.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::get_max_temp_for_current_round() const –> double

get_min_temp_for_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the minimum temperature, given the round.

Round must be set, and greater than zero. The base class version of this function just returns min_temperature_, but this can be overridden if a derived class wants to do something more complicated.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::get_min_temp_for_current_round() const –> double

max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → int

Get the total nunmber of rounds of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::max_rounds() const –> unsigned long

max_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::max_temperature() const –> const double &

min_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator) → float

Get the maximum temperature.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::min_temperature() const –> const double &

set_current_round(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, setting: int) → None

Set the index of the current round of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_current_round(const unsigned long) –> void

set_max_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, setting: int) → None

Set the total nunmber of rounds of simulated annealing.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_max_rounds(const unsigned long) –> void

set_max_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, temp_in: float) → None

Set the maximum temperature for the run.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_max_temperature(const double &) –> void

set_min_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_TemperatureScheduleGenerator, temp_in: float) → None

Set the minimum temperature for the run.

C++: protocols::helical_bundle_predict::HBP_TemperatureScheduleGenerator::set_min_temperature(const double &) –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication

Bases: pybind11_object

The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks.

align_to_native_pose(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, pose: pyrosetta.rosetta.core.pose.Pose) → float

Given a pose, align it to the native pose.

Throws an error if there’s a mismatch between the pose lengths or mainchain atom counts.

RMSD to native.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose(class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, : pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication) → pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::operator=(const class protocols::helical_bundle_predict::HelicalBundlePredictApplication &) –> class protocols::helical_bundle_predict::HelicalBundlePredictApplication &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication) → pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HelicalBundlePredictApplication>

static create_centroid_move_generator() → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Create a new move generator. Static, so this can be called from other classes (e.g.

HelicalBundlePredictApplication_MPI.)

Triggers read from disk!

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_centroid_move_generator() –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_MoveGenerator>

static create_centroid_scorefunction() → pyrosetta.rosetta.core.scoring.ScoreFunction

Create the scorefunction used during centroid mode.

Reads from disk! Do not use repeatedly! Store the result rather than regenerating it!

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_centroid_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

create_final_fullatom_refinement_move_generator(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication) → pyrosetta.rosetta.protocols.helical_bundle_predict.HBP_MoveGenerator

Create the move generator used for the final fullatom refinement step.

Not static, since it depends on the options_ object.

In its current form, this should not trigger a read from disk.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_final_fullatom_refinement_move_generator() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HBP_MoveGenerator>

static create_fullatom_scorefunction() → pyrosetta.rosetta.core.scoring.ScoreFunction

Create the scorefunction used during fullatom mode.

Reads from disk! Do not use repeatedly! Store the result rather than regenerating it!

This returns whatever the current default fullatom scorefunction is, currently. This function is here to make it easy to hard-code a specialized scorefunction in the future if necessary.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_fullatom_scorefunction() –> class std::shared_ptr<class core::scoring::ScoreFunction>

run(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication) → None

Actually run the application and produce output.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::run() –> void

set_native(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, native: pyrosetta.rosetta.core.pose.Pose) → None

Set the native pose.

Does not clone the input; sets owning pointer directly.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_native(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nstruct(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, nstruct_in: int) → None

Set the number of repeats to try.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_nstruct(const unsigned long) –> void

set_output_format(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, type: pyrosetta.rosetta.core.import_pose.FileType) → None

Set the output format. (Automatically sets extension.)

This one sets silent output to false.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_output_format(const enum core::import_pose::FileType) –> void

set_output_prefix_and_suffix(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication, prefix: str, suffix: str) → None

Set the prefix and suffix for output.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_output_prefix_and_suffix(const std::string &, const std::string &) –> void

set_silent_output(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplication) → None

Indicate that we’re using silent output. This overrides set_ouput_format(), and

sets the extension automatically.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_silent_output() –> void

class pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions

Bases: pybind11_object

Options for the application.

Prevents repeated calls to the global options system.

Vikram K. Mulligan (vmulligan.org).

assign(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, : pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::operator=(const class protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions &) –> class protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions &

centroid_max_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → float

Get the max temperature during simulated annealing steps in centroid mode.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_max_temperature() const –> const double &

centroid_min_temperature(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → float

Get the min temperature during simulated annealing steps in centroid mode.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::centroid_min_temperature() const –> const double &

clone(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions

Clone operator: copy this object and return a smart pointer to the copy.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::clone() const –> class std::shared_ptr<class protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions>

do_fullatom_refinement(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → bool

Will be doing fullatom refinement?

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::do_fullatom_refinement() const –> bool

fasta_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the file containing the sequence.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file() const –> const std::string &

fasta_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the contents of the FASTA file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fasta_file_contents() const –> const std::string &

fullatom_fast_relax_rounds(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → int

If we are doing fullatom refinement, how many rounds of FastRelax should we apply?

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_fast_relax_rounds() const –> unsigned long

fullatom_find_disulfides(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → bool

If we are doing fullatom refinement, should we try disulfide permutations?

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::fullatom_find_disulfides() const –> bool

helix_assignment_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the file containing the helix assignments.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file() const –> const std::string &

helix_assignment_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the contents of the helix assignment file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::helix_assignment_file_contents() const –> const std::string &

initialize_from_options(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → None

Read from the options system to initialize this object.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::initialize_from_options() –> void

native_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the native filename.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::native_file() const –> const std::string &

nstruct(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → int

Get the number of repeated applications of this protocol.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::nstruct() const –> unsigned long

num_simulated_annealing_rounds_centroid(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → int

Get the number of simulated annealing rounds in centroid mode.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_simulated_annealing_rounds_centroid() const –> unsigned long

num_steps_per_simulated_annealing_round_centroid(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → int

Get the number of steps per simulated annealing round in centroid mode.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::num_steps_per_simulated_annealing_round_centroid() const –> unsigned long

psipred_alpha_helix_prob_cutoff(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → float

Get the probability cutoff above which a position will be assigned to being left-handed alpha helix.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::psipred_alpha_helix_prob_cutoff() const –> double

psipred_assignment_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the file containing PsiPred predictions.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::psipred_assignment_file() const –> const std::string &

psipred_assignment_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the contents of the PsiPred assignment file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::psipred_assignment_file_contents() const –> const std::string &

psipred_beta_strand_prob_cutoff(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → float

Get the probability cutoff above which a position will be assigned to being beta strand.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::psipred_beta_strand_prob_cutoff() const –> double

read_inputs(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → None

Given input filenames, read the files.

INVOLVES READS FROM DISK! WARNING!

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::read_inputs() –> void

static register_options() → None

Indicate which commandline flags are relevant (i.e. which should be listed with the –help flag).

This is a static function that must be called BEFORE devel_init().

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::register_options() –> void

rmsd_residues_to_ignore_native(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get the residues to ignore in the native pose when setting up the alignment for RMSD.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_native() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rmsd_residues_to_ignore_prediction(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → pyrosetta.rosetta.utility.vector1_unsigned_long

Get the residues to ignore in the generated poses when setting up the alignment for RMSD.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::rmsd_residues_to_ignore_prediction() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

sequence_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions) → str

Get the contents of the sequence file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::sequence_file_contents() const –> const std::string &

set_fasta_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, file_in: str) → None

Set the file containing the FASTA sequence.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_fasta_file(const std::string &) –> void

set_fasta_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, contents_in: str) → None

Set the contents of the FASTA file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_fasta_file_contents(const std::string &) –> void

set_helix_assignment_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, file_in: str) → None

Set the file containing the helix assignments.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_helix_assignment_file(const std::string &) –> void

set_helix_assignment_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, contents_in: str) → None

Set the contents of the helix assignment file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_helix_assignment_file_contents(const std::string &) –> void

set_psipred_assignment_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, contents_in: str) → None

Set the contents of the PsiPred assignment file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_psipred_assignment_file_contents(const std::string &) –> void

set_psipred_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, psipred_file_in: str) → None

Set the file containing the PsiPred secondary structure predictions.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_psipred_file(const std::string &) –> void

set_rmsd_residues_to_ignore_native(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, input: pyrosetta.rosetta.utility.vector1_long) → None

Get the residues to ignore in the native pose when setting up the alignment for RMSD.

Throws errors if any are zero or negative.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_native(const class utility::vector1<long, class std::allocator<long> > &) –> void

set_rmsd_residues_to_ignore_prediction(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, input: pyrosetta.rosetta.utility.vector1_long) → None

Get the residues to ignore in the generated poses when setting up the alignment for RMSD.

Throws errors if any are zero or negative.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_rmsd_residues_to_ignore_prediction(const class utility::vector1<long, class std::allocator<long> > &) –> void

set_sequence_file(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, file_in: str) → None

Set the file containing the full-basename sequence.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_sequence_file(const std::string &) –> void

set_sequence_file_contents(self: pyrosetta.rosetta.protocols.helical_bundle_predict.HelicalBundlePredictApplicationOptions, contents_in: str) → None

Set the contents of the seqeunce file.

C++: protocols::helical_bundle_predict::HelicalBundlePredictApplicationOptions::set_sequence_file_contents(const std::string &) –> void