helical_bundle

Bindings for protocols::helical_bundle namespace

class pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters

Bases: pybind11_builtins.pybind11_object

Enum for relevant parameters.

If you add to this list, update the parameter_name_from_enum() function, the short_parameter_description_from_enum() function, the parameter_units_from_enum() function, the parameter_type_from_enum() function, the parameter_properties_from_enum() function, and the parameter_description_from_enum() function.

Members:

BPC_r0

BPC_omega0

BPC_delta_omega0

BPC_delta_omega1

BPC_delta_t

BPC_z0_offset

BPC_z1_offset

BPC_epsilon

BPC_last_parameter_to_be_sampled

BPC_residues_per_repeat

BPC_repeating_unit_offset

BPC_atoms_per_residue

BPC_r1_peratom

BPC_omega1

BPC_z1

BPC_delta_omega1_peratom

BPC_delta_z1_peratom

BPC_invert_helix

BPC_set_dihedrals

BPC_set_bondangles

BPC_set_bondlengths

BPC_unknown_parameter

BPC_end_of_list

BPC_atoms_per_residue = <BPC_Parameters.BPC_atoms_per_residue: 11>
BPC_delta_omega0 = <BPC_Parameters.BPC_delta_omega0: 3>
BPC_delta_omega1 = <BPC_Parameters.BPC_delta_omega1: 4>
BPC_delta_omega1_peratom = <BPC_Parameters.BPC_delta_omega1_peratom: 15>
BPC_delta_t = <BPC_Parameters.BPC_delta_t: 5>
BPC_delta_z1_peratom = <BPC_Parameters.BPC_delta_z1_peratom: 16>
BPC_end_of_list = <BPC_Parameters.BPC_unknown_parameter: 21>
BPC_epsilon = <BPC_Parameters.BPC_epsilon: 8>
BPC_invert_helix = <BPC_Parameters.BPC_invert_helix: 17>
BPC_last_parameter_to_be_sampled = <BPC_Parameters.BPC_epsilon: 8>
BPC_omega0 = <BPC_Parameters.BPC_omega0: 2>
BPC_omega1 = <BPC_Parameters.BPC_omega1: 13>
BPC_r0 = <BPC_Parameters.BPC_r0: 1>
BPC_r1_peratom = <BPC_Parameters.BPC_r1_peratom: 12>
BPC_repeating_unit_offset = <BPC_Parameters.BPC_repeating_unit_offset: 10>
BPC_residues_per_repeat = <BPC_Parameters.BPC_residues_per_repeat: 9>
BPC_set_bondangles = <BPC_Parameters.BPC_set_bondangles: 19>
BPC_set_bondlengths = <BPC_Parameters.BPC_set_bondlengths: 20>
BPC_set_dihedrals = <BPC_Parameters.BPC_set_dihedrals: 18>
BPC_unknown_parameter = <BPC_Parameters.BPC_unknown_parameter: 21>
BPC_z0_offset = <BPC_Parameters.BPC_z0_offset: 6>
BPC_z1 = <BPC_Parameters.BPC_z1: 14>
BPC_z1_offset = <BPC_Parameters.BPC_z1_offset: 7>
property name
class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_torsion_to_fix(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, residue_index: int, torsion_index: int, torsion_value: float) None

Add a mainchain torsion to fix, and that torsion’s value.

The residue_index is the index of the residue in the repeating unit (1st, 2nd, 3rd, etc.). The torsion_index is the mainchain torsion index in this residue, and the torsion_value is the value at which to fix this residue.

C++: protocols::helical_bundle::BackboneGridSampler::add_torsion_to_fix(const unsigned long, const unsigned long, const double &) –> void

add_torsion_to_sample(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, residue_index: int, torsion_index: int, start_of_range: float, end_of_range: float, samples: int) None

Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples.

The residue_index is the index in the repeating unit (1st residue, 2nd residue, etc.). The torsion_index is the mainchain torsion index in this residue. Sampled values will go from start_of_range to end_of_range, with the total number of samples given by the samples parameter. If the range is -180 to 180, the samples are adjusted so that 180 is not sampled twice.

C++: protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample(const unsigned long, const unsigned long, const double &, const double &, const unsigned long) –> void

apply(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::BackboneGridSampler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, : pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler

C++: protocols::helical_bundle::BackboneGridSampler::operator=(const class protocols::helical_bundle::BackboneGridSampler &) –> class protocols::helical_bundle::BackboneGridSampler &

cap_ends(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Return whether the ends should be capped (N-acetyl, C-methylamide).

C++: protocols::helical_bundle::BackboneGridSampler::cap_ends() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BackboneGridSampler::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BackboneGridSampler::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) str

C++: protocols::helical_bundle::BackboneGridSampler::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

max_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) int

Get the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

C++: protocols::helical_bundle::BackboneGridSampler::max_samples() const –> unsigned long

static mover_name() str

C++: protocols::helical_bundle::BackboneGridSampler::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

nres(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) int

Get the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you’d have twice this number of resiudes.

C++: protocols::helical_bundle::BackboneGridSampler::nres() const –> unsigned long

nstruct_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Get the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

C++: protocols::helical_bundle::BackboneGridSampler::nstruct_mode() const –> bool

nstruct_repeats(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) int

Get the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover’s sampling with another, similar mover’s sampling.

C++: protocols::helical_bundle::BackboneGridSampler::nstruct_repeats() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::helical_bundle::BackboneGridSampler::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pdb_output(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Returns whether the mover dumps pdbs or not.

C++: protocols::helical_bundle::BackboneGridSampler::pdb_output() const –> bool

pdb_prefix(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) str

Access the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

C++: protocols::helical_bundle::BackboneGridSampler::pdb_prefix() –> std::string

peptide_stub_mover_initialized(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Has the PeptideStubMover been initialized?

C++: protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_initialized() const –> bool

prescoring_filter_exists(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Returns “true” if and only if a preselection filter has been assigned.

C++: protocols::helical_bundle::BackboneGridSampler::prescoring_filter_exists() const –> bool

prescoring_mover_exists(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Returns “true” if and only if a preselection mover has been assigned.

C++: protocols::helical_bundle::BackboneGridSampler::prescoring_mover_exists() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::helical_bundle::BackboneGridSampler::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::BackboneGridSampler::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_and_initialize_data(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) None
Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and

initialize them based on the value of residues_per_repeat_.

C++: protocols::helical_bundle::BackboneGridSampler::reset_and_initialize_data() –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) int

Get the number of residues per repeat.

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

resname(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, res_index: int) str

Get the residue type.

Returns the residue type (full name string) for the nth residue in the list of residues defining the repeating unit.

C++: protocols::helical_bundle::BackboneGridSampler::resname(const unsigned long) const –> std::string

selection_low(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Returns whether the selection should be for the lowest score value (true) or highest (false).

C++: protocols::helical_bundle::BackboneGridSampler::selection_low() –> bool

set_cap_ends(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, cap: bool) None

Set whether then ends should be capped (N-acetyl, C-methylamide).

C++: protocols::helical_bundle::BackboneGridSampler::set_cap_ends(bool) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_max_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: int) None

Set the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

C++: protocols::helical_bundle::BackboneGridSampler::set_max_samples(const unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nres(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, nres_in: int) None

Set the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you’d have twice this number of resiudes.

C++: protocols::helical_bundle::BackboneGridSampler::set_nres(const unsigned long) –> void

set_nstruct_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: bool) None

Set the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

C++: protocols::helical_bundle::BackboneGridSampler::set_nstruct_mode(const bool &) –> void

set_nstruct_repeats(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: int) None

Set the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover’s sampling with another, similar mover’s sampling.

C++: protocols::helical_bundle::BackboneGridSampler::set_nstruct_repeats(const unsigned long) –> void

set_pdb_output(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: bool) None

Set whether the mover dumps pdbs or not.

C++: protocols::helical_bundle::BackboneGridSampler::set_pdb_output(const bool) –> void

set_pdb_prefix(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, prefix: str) None

Sets the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

C++: protocols::helical_bundle::BackboneGridSampler::set_pdb_prefix(const std::string &) –> void

set_prescoring_filter(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.

See the pre_scoring_filter_ private member variable for details.

C++: protocols::helical_bundle::BackboneGridSampler::set_prescoring_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

set_prescoring_mover(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.

Note: if this is used, there is no guarantee that the resulting geometry will still lie within the parameter space. (That is, this mover could move the backbone.)

C++: protocols::helical_bundle::BackboneGridSampler::set_prescoring_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

set_residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: int) None

Set the number of residues per repeat.

This resets the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and must therefore be called BEFORE setting up the torsions to sample, torsions to fix, or residue types.

C++: protocols::helical_bundle::BackboneGridSampler::set_residues_per_repeat(const unsigned long) –> void

set_resname(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, res_index: int, resname_in: str) None

Set the residue type.

Sets the residue type for the nth residue in the list of residues defining the repeating unit.

C++: protocols::helical_bundle::BackboneGridSampler::set_resname(const unsigned long, const std::string &) –> void

set_selection_low(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, val: bool) None

Sets whether the selection should be for the lowest score value (true) or highest (false).

C++: protocols::helical_bundle::BackboneGridSampler::set_selection_low(const bool) –> void

set_sfxn(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Sets the scorefunction for this mover.

This must be done before calling the apply() function.

C++: protocols::helical_bundle::BackboneGridSampler::set_sfxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_up_peptide_stub_mover(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) None

Set up the PeptideStubMover object that will be used to build geometry.

C++: protocols::helical_bundle::BackboneGridSampler::set_up_peptide_stub_mover() –> void

sfxn_set(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler) bool

Returns whether the scorefunction has been set.

C++: protocols::helical_bundle::BackboneGridSampler::sfxn_set() const –> bool

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator, : pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator) pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator

C++: protocols::helical_bundle::BackboneGridSamplerCreator::operator=(const class protocols::helical_bundle::BackboneGridSamplerCreator &) –> class protocols::helical_bundle::BackboneGridSamplerCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BackboneGridSamplerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator) str

C++: protocols::helical_bundle::BackboneGridSamplerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::BackboneGridSamplerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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

initialize_data(self: pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper, torsions_to_sample: pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_std_allocator_std_pair_unsigned_long_std_pair_std_pair_double_double_unsigned_long_t) None

Initialize this object from an object passed from the BackboneGridSampler mover.

C++: protocols::helical_bundle::BackboneGridSamplerHelper::initialize_data(const class utility::vector1<class utility::vector1<struct std::pair<unsigned long, struct std::pair<struct std::pair<double, double>, unsigned long> >, class std::allocator<struct std::pair<unsigned long, struct std::pair<struct std::pair<double, double>, unsigned long> > > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, struct std::pair<struct std::pair<double, double>, unsigned long> >, class std::allocator<struct std::pair<unsigned long, struct std::pair<struct std::pair<double, double>, unsigned long> > > > > > &) –> 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.BundleGridSampler

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_helix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) int

Add options for a new helix

Return value is the current total number of helices after the addition.

C++: protocols::helical_bundle::BundleGridSampler::add_helix() –> unsigned long

apply(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::BundleGridSampler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, : pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler

C++: protocols::helical_bundle::BundleGridSampler::operator=(const class protocols::helical_bundle::BundleGridSampler &) –> class protocols::helical_bundle::BundleGridSampler &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BundleGridSampler::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BundleGridSampler::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) str

C++: protocols::helical_bundle::BundleGridSampler::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

helix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, helix_index: int) protocols::helical_bundle::MakeBundleHelix

Access the mover that makes one of the helices (non-const):

C++: protocols::helical_bundle::BundleGridSampler::helix(const unsigned long) –> class std::shared_ptr<class protocols::helical_bundle::MakeBundleHelix>

helix_cop(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, helix_index: int) protocols::helical_bundle::MakeBundleHelix

Access the mover that makes one of the helices (const):

C++: protocols::helical_bundle::BundleGridSampler::helix_cop(const unsigned long) const –> class std::shared_ptr<const class protocols::helical_bundle::MakeBundleHelix>

increment_helix_count(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) None

Increments the number of helices that have been defined.

C++: protocols::helical_bundle::BundleGridSampler::increment_helix_count() –> void

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

max_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) int

Get the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

C++: protocols::helical_bundle::BundleGridSampler::max_samples() const –> unsigned long

static mover_name() str

C++: protocols::helical_bundle::BundleGridSampler::mover_name() –> std::string

n_helices(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) int

Returns the number of helices that have been defined.

C++: protocols::helical_bundle::BundleGridSampler::n_helices() const –> unsigned long

static name() str

C++: protocols::moves::Mover::name() –> std::string

nstruct_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Get the nstruct mode.

If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.

C++: protocols::helical_bundle::BundleGridSampler::nstruct_mode() const –> bool

nstruct_repeats(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) int

Get the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. This allows combinatorially combining this mover’s sampling with another, similar mover’s sampling.

C++: protocols::helical_bundle::BundleGridSampler::nstruct_repeats() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::helical_bundle::BundleGridSampler::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pdb_output(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Returns whether the mover dumps pdbs or not.

C++: protocols::helical_bundle::BundleGridSampler::pdb_output() const –> bool

pdb_prefix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) str

Access the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

C++: protocols::helical_bundle::BundleGridSampler::pdb_prefix() –> std::string

preselection_filter_exists(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Returns “true” if and only if a preselection filter has been assigned.

C++: protocols::helical_bundle::BundleGridSampler::preselection_filter_exists() const –> bool

preselection_mover_exists(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Returns “true” if and only if a preselection mover has been assigned.

C++: protocols::helical_bundle::BundleGridSampler::preselection_mover_exists() const –> bool

provide_citation_info(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::helical_bundle::BundleGridSampler::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::BundleGridSampler::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Get the reset mode.

If true (default), the pose is reset before generating bundles. If false, it is not.

C++: protocols::helical_bundle::BundleGridSampler::reset_mode() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

selection_low(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Returns whether the selection should be for the lowest score value (true) or highest (false).

C++: protocols::helical_bundle::BundleGridSampler::selection_low() –> bool

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_default_crick_params_file(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, default_crick_file: str) None

Set the default Crick params file.

This is used unless overridden on a helix-by-helix basis.

Triggers a read from disk!

C++: protocols::helical_bundle::BundleGridSampler::set_default_crick_params_file(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_max_samples(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: int) None

Set the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

C++: protocols::helical_bundle::BundleGridSampler::set_max_samples(const unsigned long) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_nstruct_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: bool) None

Set the nstruct mode.

If true, each job samples one set of Crick parameters. If false, every job samples every set of Crick parameters. False by default.

C++: protocols::helical_bundle::BundleGridSampler::set_nstruct_mode(const bool &) –> void

set_nstruct_repeats(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: int) None

Set the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of Crick parameters. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same Crick parameters. This allows combinatorially combining this mover’s sampling with another, similar mover’s sampling.

C++: protocols::helical_bundle::BundleGridSampler::set_nstruct_repeats(const unsigned long) –> void

set_pdb_output(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: bool) None

Set whether the mover dumps pdbs or not.

C++: protocols::helical_bundle::BundleGridSampler::set_pdb_output(const bool) –> void

set_pdb_prefix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, prefix: str) None

Sets the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

C++: protocols::helical_bundle::BundleGridSampler::set_pdb_prefix(const std::string &) –> void

set_preselection_filter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, filter: pyrosetta.rosetta.protocols.filters.Filter) None

Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.

See the pre_selection_filter_ private member variable for details.

C++: protocols::helical_bundle::BundleGridSampler::set_preselection_filter(class std::shared_ptr<class protocols::filters::Filter>) –> void

set_preselection_mover(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, mover: pyrosetta.rosetta.protocols.moves.Mover) None

Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.

Note: if this is used, there is no guarantee that the resulting geometry will still lie within the parameter space. (That is, this mover could move the backbone.)

C++: protocols::helical_bundle::BundleGridSampler::set_preselection_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

set_reset_mode(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: bool) None

Set the reset mode.

If true (default), the pose is reset before generating bundles. If false, it is not.

C++: protocols::helical_bundle::BundleGridSampler::set_reset_mode(const bool) –> void

set_selection_low(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, val: bool) None

Sets whether the selection should be for the lowest score value (true) or highest (false).

C++: protocols::helical_bundle::BundleGridSampler::set_selection_low(const bool) –> void

set_sfxn(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Sets the scorefunction for this mover.

This must be done before calling the apply() function.

C++: protocols::helical_bundle::BundleGridSampler::set_sfxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler, use_degrees: bool) None

Set whether we’re using degrees (true) or radians (false)

C++: protocols::helical_bundle::BundleGridSampler::set_use_degrees(const bool) –> void

sfxn_set(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Returns whether the scorefunction has been set.

C++: protocols::helical_bundle::BundleGridSampler::sfxn_set() const –> bool

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSampler) bool

Get whether we’re using degrees (true) or radians (false)

C++: protocols::helical_bundle::BundleGridSampler::use_degrees() const –> bool

class pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator, : pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator) pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator

C++: protocols::helical_bundle::BundleGridSamplerCreator::operator=(const class protocols::helical_bundle::BundleGridSamplerCreator &) –> class protocols::helical_bundle::BundleGridSamplerCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::BundleGridSamplerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator) str

C++: protocols::helical_bundle::BundleGridSamplerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::BundleGridSamplerCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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.BPC_Parameters) str

Return the name of a DoF type given its enum.

C++: protocols::helical_bundle::BundleGridSamplerHelper::DoF_name(const enum protocols::helical_bundle::BPC_Parameters &) const –> 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.BPC_Parameters

Returns the DoF type of the specified DoF.

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

add_DoF(self: pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper, doftype: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters, 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::BPC_Parameters, 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.BundleParametrizationCalculator

Bases: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

BundleParametrizationCalculator class, used for parametric helical bundle backbone generation.

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, : pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

C++: protocols::helical_bundle::BundleParametrizationCalculator::operator=(const class protocols::helical_bundle::BundleParametrizationCalculator &) –> class protocols::helical_bundle::BundleParametrizationCalculator &

boolean_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

Accesses a boolean-valued parameter.

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::boolean_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::BooleanValuedParameter>

boolean_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) pyrosetta.rosetta.core.conformation.parametric.BooleanValuedParameter

Accesses a boolean-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a BooleanValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::boolean_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::BooleanValuedParameter>

build_helix(*args, **kwargs)

Overloaded function.

  1. build_helix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, pose: pyrosetta.rosetta.core.pose.Pose) -> bool

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object “pose” is replaced with a new helix if this operation succeeds.

C++: protocols::helical_bundle::BundleParametrizationCalculator::build_helix(class core::pose::Pose &) const –> bool

  1. build_helix(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, helix_start: int, helix_end: int) -> bool

Attempts to build a helix based on the current Crick parameters.

Returns true for FAILURE and false for SUCCESS. The object “pose” is replaced with a new helix if this operation succeeds.

This version takes parameters for the start and end of the helix.

C++: protocols::helical_bundle::BundleParametrizationCalculator::build_helix(class core::pose::Pose &, const unsigned long, const unsigned long) const –> bool

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

Copy this object ( allocate actual memory for it )

C++: protocols::helical_bundle::BundleParametrizationCalculator::clone() const –> class std::shared_ptr<class core::conformation::parametric::ParametrizationCalculator>

copy_params_from_previous_helices_makebundlehelix_style(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, prev_helices_pose: pyrosetta.rosetta.core.pose.Pose) bool

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

This function assumes that the input pose consists only of previous helices, and stores N ParametersSet objects for N helices, each with 1 Parameters object contained.

Returns true for failure, false for success.

C++: protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(const class core::pose::Pose &) –> bool

static copy_params_from_previous_helices_perturbbundle_style(paramset: pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParametersSet, copy_from_helix_index: int, parameter_type: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters, parameter_to_copy_to: pyrosetta.rosetta.core.conformation.parametric.RealValuedParameter, current_helix_params: pyrosetta.rosetta.protocols.helical_bundle.parameters.BundleParameters) bool

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before build_helix().

This function assumes that the input pose is the whole shebang passed to the PerturbBundle mover. Unlike copy_params_from_previous_helices_makebundlehelix_style(), this functon does not modify the BundleParametrizationCalculator. Instead it copies the parameter value for the given parameter from the indicated previous helix to the indicated parameter object.

Returns true for failure, false for success.

C++: protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_perturbbundle_style(class std::shared_ptr<const class protocols::helical_bundle::parameters::BundleParametersSet>, const unsigned long, const enum protocols::helical_bundle::BPC_Parameters, class std::shared_ptr<class core::conformation::parametric::RealValuedParameter>, class std::shared_ptr<const class protocols::helical_bundle::parameters::BundleParameters>) –> bool

copy_unset_params_from_globals(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, global_calculator: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) None

Copy the parameter values for parameters that have not been set from the global parameters.

This function should be called before build_helix().

C++: protocols::helical_bundle::BundleParametrizationCalculator::copy_unset_params_from_globals(class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>) –> void

get_self_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator

C++: core::conformation::parametric::ParametrizationCalculator::get_self_ptr() –> class std::shared_ptr<class core::conformation::parametric::ParametrizationCalculator>

get_self_weak_ptr(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) pyrosetta.rosetta.std.weak_ptr_core_conformation_parametric_ParametrizationCalculator_t

C++: core::conformation::parametric::ParametrizationCalculator::get_self_weak_ptr() –> class std::weak_ptr<class core::conformation::parametric::ParametrizationCalculator>

init_from_file(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, filename: str) None

Read a Crick params file and initialize this calculator.

Triggers a read from disk!

C++: protocols::helical_bundle::BundleParametrizationCalculator::init_from_file(const std::string &) –> void

parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter.

C++: core::conformation::parametric::ParametrizationCalculator::parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::Parameter>

parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) pyrosetta.rosetta.core.conformation.parametric.Parameter

Access a parameter.

Const-access

C++: core::conformation::parametric::ParametrizationCalculator::parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::Parameter>

static parameter_description_from_enum(param_enum: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) str

Given a BPC_Parameters enum, get a short lay-language description (used for annotating output) of the parameter.

Returns “INVALID!!!” if invalid.

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_description_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> const std::string &

static parameter_enum_from_name(name: str) pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters

Get the BPC_Parameters enum from the parameter name.

Returns BPC_unknown_parameter if this can’t be parsed.

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_enum_from_name(const std::string &) –> enum protocols::helical_bundle::BPC_Parameters

static parameter_name_from_enum(param_type: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) str

Get the parameter name from the BPC_Parameters enum.

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_name_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> const std::string &

static parameter_properties_from_enum(param_enum: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) pyrosetta.rosetta.core.conformation.parametric.ParameterizationCalculatorProperties
Given a BPC_Parameters enum, get whether this parameter is one that the user can set, whether it can be sampled, whether it can be perturbed, and whether it’s global

for a ParametersSet (helical bundle).

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_properties_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> const struct core::conformation::parametric::ParameterizationCalculatorProperties &

static parameter_type_from_enum(param_enum: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) pyrosetta.rosetta.core.conformation.parametric.ParameterType

Get the parameter type from the BPC_Parameters enum.

Returns PT_invalid_type if invalid.

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_type_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> enum core::conformation::parametric::ParameterType

static parameter_units_from_enum(param_type: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) str

Get the parameter units from the BPC_Parameters enum.

C++: protocols::helical_bundle::BundleParametrizationCalculator::parameter_units_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> const std::string &

parameters_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator) pyrosetta.rosetta.core.conformation.parametric.Parameters

Get a const-owning pointer to the Parameters object.

C++: core::conformation::parametric::ParametrizationCalculator::parameters_cop() const –> class std::shared_ptr<const class core::conformation::parametric::Parameters>

real_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::RealValuedParameter

Accesses a real-valued parameter.

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::real_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::RealValuedParameter>

real_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::RealValuedParameter

Accesses a real-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::real_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::RealValuedParameter>

realvector_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::RealVectorValuedParameter

Accesses a realvector-valued parameter.

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::realvector_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::RealVectorValuedParameter>

realvector_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::RealVectorValuedParameter

Accesses a realvector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a RealVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::realvector_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::RealVectorValuedParameter>

repeats_per_turn(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) int

Get the number of repeats needed to go one full turn.

This is rounded UP. So for an alpha helix, with about 3.6 repeating units (residues) per turn, this function returns 4.

C++: protocols::helical_bundle::BundleParametrizationCalculator::repeats_per_turn() const –> unsigned long

residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) int

The number of residues per repeating unit.

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

residues_per_turn(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) int

The number of residues needed for one full turn.

This is repeats_per_turn() * residues_per_repeat().

C++: protocols::helical_bundle::BundleParametrizationCalculator::residues_per_turn() const –> unsigned long

set_perturbation_type_globally(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, perturbation_type_in: str) None

Set the perturbation type for all parameters.

C++: protocols::helical_bundle::BundleParametrizationCalculator::set_perturbation_type_globally(const std::string &) –> void

set_use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator, setting: bool) None

Set whether this calculator uses degrees or radians for the user-set angles.

Defaults to radians (false).

C++: protocols::helical_bundle::BundleParametrizationCalculator::set_use_degrees(const bool) –> void

static short_parameter_description_from_enum(param_type: pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters) str

Get the short parameter name from the BPC_Parameters enum.

C++: protocols::helical_bundle::BundleParametrizationCalculator::short_parameter_description_from_enum(enum protocols::helical_bundle::BPC_Parameters) –> const std::string &

size_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::SizeValuedParameter

Accesses a size-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::size_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::SizeValuedParameter>

size_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::SizeValuedParameter

Accesses a size-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::size_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::SizeValuedParameter>

sizevector_parameter(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::SizeVectorValuedParameter

Accesses a sizevector-valued parameter.

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::sizevector_parameter(const unsigned long) –> class std::shared_ptr<class core::conformation::parametric::SizeVectorValuedParameter>

sizevector_parameter_cop(self: pyrosetta.rosetta.core.conformation.parametric.ParametrizationCalculator, index: int) core::conformation::parametric::SizeVectorValuedParameter

Accesses a sizevector-valued parameter (const-access).

Returns nullptr if the parameter with the given index is not a SizeVectorValuedParameter.

C++: core::conformation::parametric::ParametrizationCalculator::sizevector_parameter_cop(const unsigned long) const –> class std::shared_ptr<const class core::conformation::parametric::SizeVectorValuedParameter>

use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) bool

Get whether this calculator expects input in degrees or radians for user-set angles.

C++: protocols::helical_bundle::BundleParametrizationCalculator::use_degrees() const –> bool

class pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter

Bases: pyrosetta.rosetta.protocols.filters.Filter

apply(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool

Actually apply the filter to a pose.

This scores the pose with the scorefunction, writes out the energy and the bundle parameters (if any) to the REPORT tracer, then applies the selected behaviour of the filter (always true, always false, or actually filtering by score).

C++: protocols::helical_bundle::BundleReporterFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() str

C++: protocols::helical_bundle::BundleReporterFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) None

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) pyrosetta.rosetta.protocols.filters.Filter
Returns an owning pointer to a new instance of this filter, with copied

variables (a copy of this filter).

C++: protocols::helical_bundle::BundleReporterFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

Computes the energy of the pose.

the energy function must be suitable for residue type set of the pose, and must be symmetric if this is a symmetric pose.

C++: protocols::helical_bundle::BundleReporterFilter::compute(const class core::pose::Pose &) const –> double

filter_behaviour(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour

Get the filter behaviour.

C++: protocols::helical_bundle::BundleReporterFilter::filter_behaviour() const –> enum protocols::helical_bundle::BundleReporterFilterBehaviour

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) pyrosetta.rosetta.protocols.filters.Filter
Returns an owning pointer to a new instance of this filter, with default

initialization (NOT a copy).

C++: protocols::helical_bundle::BundleReporterFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

generate_full_tracer_report(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, jobno: int, score: float, pose: pyrosetta.rosetta.core.pose.Pose) str

Generates the text of the full report that the filter writes out to the REPORT tracer.

Called by the APPLY function. Jobno is the RosettaScripts job number; ignored if set to 0.

C++: protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(const unsigned long, const double &, const class core::pose::Pose &) const –> std::string

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) str

C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) str

C++: protocols::helical_bundle::BundleReporterFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Parse XML (RosettaScripts) setup.

C++: protocols::helical_bundle::BundleReporterFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by filters wishing to provide citation information.

C++: protocols::filters::Filter::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::BundleReporterFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

Allows reporting of filter values to a stream.

C++: protocols::helical_bundle::BundleReporterFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sequence(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) bool

Get whether we report sequences.

C++: protocols::helical_bundle::BundleReporterFilter::report_sequence() const –> bool

report_sm(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, pose: pyrosetta.rosetta.core.pose.Pose) float

Allows reporting of the filter value to a float.

C++: protocols::helical_bundle::BundleReporterFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

score_type(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) pyrosetta.rosetta.core.scoring.ScoreType

Get the score type.

C++: protocols::helical_bundle::BundleReporterFilter::score_type() const –> enum core::scoring::ScoreType

score_type_threshold(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) float

Get the score threshold.

C++: protocols::helical_bundle::BundleReporterFilter::score_type_threshold() const –> double

scorefxn(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) pyrosetta.rosetta.core.scoring.ScoreFunction

Get the scorefunction (by owning pointer).

Non-const access.

C++: protocols::helical_bundle::BundleReporterFilter::scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_filter_behaviour(*args, **kwargs)

Overloaded function.

  1. set_filter_behaviour(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, behaviour_string: str) -> None

Set the behaviour by string.

Options are “ALWAYS_TRUE”, “ALWAYS_FALSE”, or “FILTER”.

C++: protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour(const std::string &) –> void

  1. set_filter_behaviour(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, behaviour_in: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterBehaviour) -> None

Set the behaviour by enum.

Options are brf_always_true, brf_always_false, or brf_filter_by_energy.

C++: protocols::helical_bundle::BundleReporterFilter::set_filter_behaviour(const enum protocols::helical_bundle::BundleReporterFilterBehaviour) –> void

set_report_sequence(*args, **kwargs)

Overloaded function.

  1. set_report_sequence(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) -> None

  2. set_report_sequence(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, val: bool) -> None

Set whether we report sequences.

C++: protocols::helical_bundle::BundleReporterFilter::set_report_sequence(const bool) –> void

set_score_type(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, type: pyrosetta.rosetta.core.scoring.ScoreType) None

Set the score type.

C++: protocols::helical_bundle::BundleReporterFilter::set_score_type(const enum core::scoring::ScoreType &) –> void

set_score_type_threshold(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, val: float) None

Set the score threshold.

C++: protocols::helical_bundle::BundleReporterFilter::set_score_type_threshold(const double &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, scorefxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Set the scorefunction.

C++: protocols::helical_bundle::BundleReporterFilter::set_scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_use_threeletter(*args, **kwargs)

Overloaded function.

  1. set_use_threeletter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) -> None

  2. set_use_threeletter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter, val: bool) -> None

Set whether we report three-letter codes.

C++: protocols::helical_bundle::BundleReporterFilter::set_use_threeletter(const bool) –> void

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) None

C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

use_threeletter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) bool

Get whether we report three-letter codes.

C++: protocols::helical_bundle::BundleReporterFilter::use_threeletter() const –> bool

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

brf_always_false = <BundleReporterFilterBehaviour.brf_always_false: 2>
brf_always_true = <BundleReporterFilterBehaviour.brf_always_true: 1>
brf_filter_by_energy = <BundleReporterFilterBehaviour.brf_filter_by_energy: 3>
brf_undefined = <BundleReporterFilterBehaviour.brf_undefined: 4>
property name
class pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator

Bases: pyrosetta.rosetta.protocols.filters.FilterCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator, : pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator) pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator

C++: protocols::helical_bundle::BundleReporterFilterCreator::operator=(const class protocols::helical_bundle::BundleReporterFilterCreator &) –> class protocols::helical_bundle::BundleReporterFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator) pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::helical_bundle::BundleReporterFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator) str

C++: protocols::helical_bundle::BundleReporterFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::BundleReporterFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::FitSimpleHelix::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, : pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix

C++: protocols::helical_bundle::FitSimpleHelix::operator=(const class protocols::helical_bundle::FitSimpleHelix &) –> class protocols::helical_bundle::FitSimpleHelix &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::FitSimpleHelix::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::FitSimpleHelix::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_crick_parameters(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, r1_out: pyrosetta.rosetta.utility.vector1_double, omega1_out: float, z1_out: float, delta_omega1_out: pyrosetta.rosetta.utility.vector1_double, delta_z1_out: pyrosetta.rosetta.utility.vector1_double) None

Function to retrieve the final values of the helical parameters, post-fit.

Call this function after the “apply” function, and pass it containers for the data to be retrieved.

C++: protocols::helical_bundle::FitSimpleHelix::get_crick_parameters(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> > &) const –> void

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) str

C++: protocols::helical_bundle::FitSimpleHelix::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::helical_bundle::FitSimpleHelix::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::helical_bundle::FitSimpleHelix::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::FitSimpleHelix::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_residue(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) int

Get the reference residue index in the repeating unit.

C++: protocols::helical_bundle::FitSimpleHelix::reference_residue() const –> unsigned long

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix) int

Get the number of residues per repeating unit in the helix.

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

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_delta_omega1_guesses(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, delta_omega1_guesses_in: pyrosetta.rosetta.utility.vector1_double) None

Load in guesses for the delta_omega1 values (optional during fitter setup).

C++: protocols::helical_bundle::FitSimpleHelix::set_delta_omega1_guesses(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_delta_z1_guesses(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, delta_z1_guesses_in: pyrosetta.rosetta.utility.vector1_double) None

Load in guesses for the delta_z1 values (optional during fitter setup).

C++: protocols::helical_bundle::FitSimpleHelix::set_delta_z1_guesses(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_initial_guesses(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, r1_initial: float, omega1_initial: float, dz1_initial: float) None

C++: protocols::helical_bundle::FitSimpleHelix::set_initial_guesses(const double &, const double &, const double &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_min_tolerance(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, min_tol_in: float) None

Set the minimizer tolerance (defaults to 1E-7, the default for many other protocols).

C++: protocols::helical_bundle::FitSimpleHelix::set_min_tolerance(const double &) –> void

set_min_type(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, min_type: str) None

Set the minimization type (e.g. dfpmin, linmin, etc.)

Defaults to dfpmin if not set.

C++: protocols::helical_bundle::FitSimpleHelix::set_min_type(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_r1_guesses(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, r1_guesses_in: pyrosetta.rosetta.utility.vector1_double) None

Load in guesses for the radii (optional during fitter setup).

C++: protocols::helical_bundle::FitSimpleHelix::set_r1_guesses(const class utility::vector1<double, class std::allocator<double> > &) –> void

set_range(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, start: int, end: int) None

C++: protocols::helical_bundle::FitSimpleHelix::set_range(const unsigned long, const unsigned long) –> void

set_reference_atom(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, ref_atom_in: str) None

Set the mainchain atom that will be fit first, and used as the reference for other mainchain atoms.

If not set, this defaults to “CA”.

C++: protocols::helical_bundle::FitSimpleHelix::set_reference_atom(const std::string &) –> void

set_reference_residue(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, ref_res_in: int) None

Set the residue in the repeating unit (1, 2, 3, etc.) that contains the reference atom.

If not set, this defaults to 1.

C++: protocols::helical_bundle::FitSimpleHelix::set_reference_residue(const unsigned long) –> void

set_residues_per_repeat(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, count_in: int) None

Set the number of residues per repeating unit in the helix.

If not set, this defaults to 1.

C++: protocols::helical_bundle::FitSimpleHelix::set_residues_per_repeat(const unsigned long) –> void

set_rms_offset(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix, rms_offset_in: float) None

Set the small float used to offset certain values in the RMS calculation to avoid zero determinants.

If fits produce bad geometry, this may need to be increased slightly.

C++: protocols::helical_bundle::FitSimpleHelix::set_rms_offset(const double &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator, : pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator) pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator

C++: protocols::helical_bundle::FitSimpleHelixCreator::operator=(const class protocols::helical_bundle::FitSimpleHelixCreator &) –> class protocols::helical_bundle::FitSimpleHelixCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::FitSimpleHelixCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator) str

C++: protocols::helical_bundle::FitSimpleHelixCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::FitSimpleHelixCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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.MakeBundle

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_helix(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) None

Function to add a helix.

This creates a MakeBundleHelix mover that will be called at apply time. Note that this function assumes that default parameter values have been set already. They cannot be set after calling this function.

C++: protocols::helical_bundle::MakeBundle::add_helix() –> void

apply(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::MakeBundle::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, : pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) pyrosetta.rosetta.protocols.helical_bundle.MakeBundle

C++: protocols::helical_bundle::MakeBundle::operator=(const class protocols::helical_bundle::MakeBundle &) –> class protocols::helical_bundle::MakeBundle &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundle::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

default_calculator(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) protocols::helical_bundle::BundleParametrizationCalculator

Access the default calculator directly.

Const access.

C++: protocols::helical_bundle::MakeBundle::default_calculator() const –> class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>

default_calculator_nonconst(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) protocols::helical_bundle::BundleParametrizationCalculator

Access the default calculator directly.

Nonconst access is potentially dangerous! Use with caution!

Used by BundleGridSampler to access the contained MakeBundle mover’s calculator directly.

C++: protocols::helical_bundle::MakeBundle::default_calculator_nonconst() –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

default_crick_params_file(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) str

Returns the default Crick params file name.

C++: protocols::helical_bundle::MakeBundle::default_crick_params_file() const –> const std::string &

default_helix_length(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) int

Returns the default number of residues per helix.

C++: protocols::helical_bundle::MakeBundle::default_helix_length() const –> unsigned long

default_residue_name(*args, **kwargs)

Overloaded function.

  1. default_residue_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, index_in_repeating_unit: int) -> str

Returns the default residue name for a particular position in the repeating unit.

C++: protocols::helical_bundle::MakeBundle::default_residue_name(const unsigned long) const –> const std::string &

  1. default_residue_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) -> pyrosetta.rosetta.utility.vector1_std_string

Returns the default residue name vector.

C++: protocols::helical_bundle::MakeBundle::default_residue_name() const –> const class utility::vector1<std::string, class std::allocator<std::string > > &

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundle::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) str

C++: protocols::helical_bundle::MakeBundle::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

helix(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, index: int) protocols::helical_bundle::MakeBundleHelix

Non-const access to helix in the bundle.

C++: protocols::helical_bundle::MakeBundle::helix(const unsigned long &) –> class std::shared_ptr<class protocols::helical_bundle::MakeBundleHelix>

helix_cop(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, index: int) protocols::helical_bundle::MakeBundleHelix

Const access to helix in the bundle.

C++: protocols::helical_bundle::MakeBundle::helix_cop(const unsigned long &) const –> class std::shared_ptr<const class protocols::helical_bundle::MakeBundleHelix>

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

initialize_default_calculator_from_default_crick_params_file(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) None

Initialize the default calculator from the deafult Crick params file.

Triggers a read from disk!

C++: protocols::helical_bundle::MakeBundle::initialize_default_calculator_from_default_crick_params_file() –> void

last_apply_failed(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) bool
Returns true or false based on whether the last call to the apply() function

failed (true) or succeeded (false).

The apply() function calls the private function set_last_apply_failed() to set this.

C++: protocols::helical_bundle::MakeBundle::last_apply_failed() const –> bool

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::helical_bundle::MakeBundle::mover_name() –> std::string

n_helices(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) int

Returns the number of helices.

Note that this is not multiplied by the number of symmetry repeats. That is, if the bundle has 3-fold symmetry and 2 helices are defined, there will be 6 helices in the final structure, but this function would still return 2.

C++: protocols::helical_bundle::MakeBundle::n_helices() const –> unsigned long

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::helical_bundle::MakeBundle::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::helical_bundle::MakeBundle::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::MakeBundle::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_pose(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) bool
Returns a bool indicating whether the input pose will be reset prior to

building a helix.

C++: protocols::helical_bundle::MakeBundle::reset_pose() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_crick_params_file_for_helix(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, filename: str, helix_index: int) None

Set the Crick params file for a particular helix.

Triggers a read from disk!

C++: protocols::helical_bundle::MakeBundle::set_crick_params_file_for_helix(const std::string &, const unsigned long) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_default_crick_params_file(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, input_string: str) None

Set the default Crick params file name.

Triggers a read from disk!

C++: protocols::helical_bundle::MakeBundle::set_default_crick_params_file(const std::string &) –> void

set_default_helix_length(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, val: int) None

Set the default number of residues per helix

C++: protocols::helical_bundle::MakeBundle::set_default_helix_length(const unsigned long &) –> void

set_default_residue_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, names: pyrosetta.rosetta.utility.vector1_std_string) None

Set the default residue name

C++: protocols::helical_bundle::MakeBundle::set_default_residue_name(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_helix_length_for_helix(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, helix_length: int, helix_index: int) None

Set the helix length, in residues, for the Nth helix.

C++: protocols::helical_bundle::MakeBundle::set_helix_length_for_helix(const unsigned long, const unsigned long) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_reset_pose(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, reset_in: bool) None

Set whether the input pose should be reset prior to building a helix.

C++: protocols::helical_bundle::MakeBundle::set_reset_pose(const bool) –> void

set_residue_name_for_helix(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, names: pyrosetta.rosetta.utility.vector1_std_string, helix_index: int) None

Set the residue names for a given helix.

C++: protocols::helical_bundle::MakeBundle::set_residue_name_for_helix(const class utility::vector1<std::string, class std::allocator<std::string > > &, const unsigned long) –> void

set_symmetry(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, symmetry_in: int) None

Set the symmetry of the bundle.

See bundle_symmetry_ member variable for details.

C++: protocols::helical_bundle::MakeBundle::set_symmetry(const unsigned long) –> void

set_symmetry_copies(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, symmetry_copies_in: int) None

Set how many of the symmetry copies actually get generated.

See bundle_symmetry_copies_ member variable for details.

C++: protocols::helical_bundle::MakeBundle::set_symmetry_copies(const unsigned long) –> void

set_symmetry_options_from_tag(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, tag: pyrosetta.rosetta.utility.tag.Tag) None

Set symmetry and symmetry_copies options based on an input tag.

C++: protocols::helical_bundle::MakeBundle::set_symmetry_options_from_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

set_use_degrees(*args, **kwargs)

Overloaded function.

  1. set_use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) -> None

  2. set_use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle, val: bool) -> None

Set whether we’re using degrees (true) or radians (false).

C++: protocols::helical_bundle::MakeBundle::set_use_degrees(const bool) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

symmetry(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) int

Get the symmetry of the bundle.

See bundle_symmetry_ member variable for details.

C++: protocols::helical_bundle::MakeBundle::symmetry() const –> unsigned long

symmetry_copies(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) int

Get how many of the symmetry copies actually get generated.

See bundle_symmetry_copies_ member variable for details.

C++: protocols::helical_bundle::MakeBundle::symmetry_copies() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) bool

Get whether we’re using degrees (true) or radians (false).

C++: protocols::helical_bundle::MakeBundle::use_degrees() const –> bool

class pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator, : pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator) pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator

C++: protocols::helical_bundle::MakeBundleCreator::operator=(const class protocols::helical_bundle::MakeBundleCreator &) –> class protocols::helical_bundle::MakeBundleCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundleCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator) str

C++: protocols::helical_bundle::MakeBundleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::MakeBundleCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::MakeBundleHelix::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, : pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix

C++: protocols::helical_bundle::MakeBundleHelix::operator=(const class protocols::helical_bundle::MakeBundleHelix &) –> class protocols::helical_bundle::MakeBundleHelix &

calculator_cop(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Const access to the calculator.

C++: protocols::helical_bundle::MakeBundleHelix::calculator_cop() const –> class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>

calculator_op(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Non-const access to the calculator.

C++: protocols::helical_bundle::MakeBundleHelix::calculator_op() –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundleHelix::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

copy_params_from_previous_helices(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, prev_helices_pose: pyrosetta.rosetta.core.pose.Pose) bool

Copy the parameter values for parameters that copy values from previous helices, from the previous helices.

This function should be called before apply().

Returns true for failure, false for success.

C++: protocols::helical_bundle::MakeBundleHelix::copy_params_from_previous_helices(const class core::pose::Pose &) –> bool

copy_unset_params_from_globals(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, global_calculator: pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator) None

Copy the parameter values for parameters that have not been set from the global parameters.

This function should be called before apply().

C++: protocols::helical_bundle::MakeBundleHelix::copy_unset_params_from_globals(class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>) –> void

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundleHelix::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) str

C++: protocols::helical_bundle::MakeBundleHelix::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

helix_length(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) int
Returns a bool indicating whether the input pose will be reset prior to

building a helix.

C++: protocols::helical_bundle::MakeBundleHelix::helix_length() const –> unsigned long

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_apply_failed(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) bool

Returns “true” if the last call to the apply function failed, false otherwise.

C++: protocols::helical_bundle::MakeBundleHelix::last_apply_failed() const –> bool

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::helical_bundle::MakeBundleHelix::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::MakeBundleHelix::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_pose(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix) bool
Returns a bool indicating whether the input pose will be reset prior to

building a helix.

C++: protocols::helical_bundle::MakeBundleHelix::reset_pose() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

residue_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, repeat_index: int) str
Get the name (full name, not 3-letter code) of one of the residue types in the repeating

unit that will make up the helix.

C++: protocols::helical_bundle::MakeBundleHelix::residue_name(const unsigned long) const –> const std::string &

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_helix_length(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, helix_length_in: int) None

Set the length of the helix, in residues.

C++: protocols::helical_bundle::MakeBundleHelix::set_helix_length(const unsigned long) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_minor_helix_params_from_file(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, filename: str) None

Set the minor helix parameters by reading them in from a file.

C++: protocols::helical_bundle::MakeBundleHelix::set_minor_helix_params_from_file(const std::string &) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_reset_pose(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, reset_in: bool) None

Set whether the input pose should be reset prior to building a helix.

C++: protocols::helical_bundle::MakeBundleHelix::set_reset_pose(const bool) –> void

set_residue_name(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix, names: pyrosetta.rosetta.utility.vector1_std_string) None

Set the residue type(s) (full name, not 3-letter code) that will make up the helix.

If there is more than one residue per repeating unit in the minor helix, one residue name must be provided for each residue in the repeating unit. Note that there is no check that the size of the residue_name_ vector matches the number of residues in the repeating unit until apply time.

C++: protocols::helical_bundle::MakeBundleHelix::set_residue_name(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator, : pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator) pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator

C++: protocols::helical_bundle::MakeBundleHelixCreator::operator=(const class protocols::helical_bundle::MakeBundleHelixCreator &) –> class protocols::helical_bundle::MakeBundleHelixCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::MakeBundleHelixCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator) str

C++: protocols::helical_bundle::MakeBundleHelixCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelixCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::MakeBundleHelixCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_helix(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, helix_index: int) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Add options for a new helix.

Return value is a smart pointer to the BundleParametrizationCalculator for the new helix, cloned from the default_calculator_.

C++: protocols::helical_bundle::PerturbBundle::add_helix(const unsigned long) –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

apply(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::PerturbBundle::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle

C++: protocols::helical_bundle::PerturbBundle::operator=(const class protocols::helical_bundle::PerturbBundle &) –> class protocols::helical_bundle::PerturbBundle &

bundleparametersset_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) int

Returns a value indicating which bundle parameters set will be used, if more than one is defined in the pose’s Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

C++: protocols::helical_bundle::PerturbBundle::bundleparametersset_index() const –> unsigned long

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundle::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

default_calculator(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Access the default calculator (nonconst access).

C++: protocols::helical_bundle::PerturbBundle::default_calculator() –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

default_calculator_cop(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Access the default calculator (const access).

C++: protocols::helical_bundle::PerturbBundle::default_calculator_cop() const –> class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundle::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) str

C++: protocols::helical_bundle::PerturbBundle::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

individual_helix_calculator(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, helix_calculator_index: int) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Access the calculator for a given helix (nonconst access).

C++: protocols::helical_bundle::PerturbBundle::individual_helix_calculator(const unsigned long) –> class std::shared_ptr<class protocols::helical_bundle::BundleParametrizationCalculator>

individual_helix_calculator_cop(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, helix_calculator_index: int) pyrosetta.rosetta.protocols.helical_bundle.BundleParametrizationCalculator

Access the calculator for a given helix (const access).

C++: protocols::helical_bundle::PerturbBundle::individual_helix_calculator_cop(const unsigned long) const –> class std::shared_ptr<const class protocols::helical_bundle::BundleParametrizationCalculator>

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::helical_bundle::PerturbBundle::mover_name() –> std::string

n_helices(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) int
Get the number of individual helices that have been configured (which is not necessarily the number

of helices in the pose, since we might only be perturbing a subset).

C++: protocols::helical_bundle::PerturbBundle::n_helices() const –> unsigned long

static name() str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::helical_bundle::PerturbBundle::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None

Provide the citation.

C++: protocols::helical_bundle::PerturbBundle::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::PerturbBundle::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_helices(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle) None

Clear the list of helices.

C++: protocols::helical_bundle::PerturbBundle::reset_helices() –> void

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_bundleparametersset_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle, val: int) None

Set which bundle parameters set will be used, if more than one is defined in the pose’s Conformation object.

A value of n indicates that the nth bundle paramets set encountered will be perturbed.

C++: protocols::helical_bundle::PerturbBundle::set_bundleparametersset_index(const unsigned long) –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator) pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator

C++: protocols::helical_bundle::PerturbBundleCreator::operator=(const class protocols::helical_bundle::PerturbBundleCreator &) –> class protocols::helical_bundle::PerturbBundleCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundleCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator) str

C++: protocols::helical_bundle::PerturbBundleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::PerturbBundleCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix, pose: pyrosetta.rosetta.core.pose.Pose) None

Actually apply the mover to the pose.

C++: protocols::helical_bundle::PerturbBundleHelix::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix

C++: protocols::helical_bundle::PerturbBundleHelix::operator=(const class protocols::helical_bundle::PerturbBundleHelix &) –> class protocols::helical_bundle::PerturbBundleHelix &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundleHelix::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundleHelix::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) str
A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) str

C++: protocols::helical_bundle::PerturbBundleHelix::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_std_allocator_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_apply_failed(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) bool

C++: protocols::helical_bundle::PerturbBundleHelix::last_apply_failed() const –> bool

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static mover_name() str

C++: protocols::helical_bundle::PerturbBundleHelix::mover_name() –> std::string

static name() str

C++: protocols::moves::Mover::name() –> std::string

parameters_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) int

Returns the index of the Parameters object in the ParametersSet object in the pose that’s being perturbed.

This Parameters object contains the Crick parameters that define the helix that’s being perturbed.

C++: protocols::helical_bundle::PerturbBundleHelix::parameters_index() const –> unsigned long

parameters_set_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix) int

Returns the index of the ParametersSet object in the pose that’s being perturbed.

This ParametersSet contains the Parameters object that defines the helix that’s being perturbed.

C++: protocols::helical_bundle::PerturbBundleHelix::parameters_set_index() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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

C++: protocols::helical_bundle::PerturbBundleHelix::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_parameters_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix, index: int) None

Sets the index of the Parameters object in the ParametersSet object in the pose that’s being perturbed.

This Parameters object contains the Crick parameters that define the helix that’s being perturbed.

C++: protocols::helical_bundle::PerturbBundleHelix::set_parameters_index(const unsigned long) –> void

set_parameters_set_index(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix, index: int) None

Sets the index of the ParametersSet object in the pose that’s being perturbed.

This ParametersSet contains the Parameters object that defines the helix that’s being perturbed.

C++: protocols::helical_bundle::PerturbBundleHelix::set_parameters_set_index(const unsigned long) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

  2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

  1. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator, : pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator) pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator

C++: protocols::helical_bundle::PerturbBundleHelixCreator::operator=(const class protocols::helical_bundle::PerturbBundleHelixCreator &) –> class protocols::helical_bundle::PerturbBundleHelixCreator &

create_mover(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator) pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::helical_bundle::PerturbBundleHelixCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator) str

C++: protocols::helical_bundle::PerturbBundleHelixCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelixCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::helical_bundle::PerturbBundleHelixCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

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_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.

The pose is just used to look up mainchain atom counts in residues.

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.get_crick_params_filename_formatted(basename: str) str
Given a Crick params filename stub (e.g. “alpha_helix_100”), get the string with the

full path and extension (e.g. “protocol_data/crick_parameters/alpha_helix_100.crick_params”).

Checks a few locations (current path, database path), so this necessarily involves a read from disk!

C++: protocols::helical_bundle::get_crick_params_filename_formatted(const std::string &) –> std::string

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 std::string &, class utility::vector1<std::string, class std::allocator<std::string > > &) –> 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 std::string &, 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.

  1. 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 std::string &, 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

  1. 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 std::string &, 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