helical_bundle¶
Bindings for protocols::helical_bundle namespace
- class pyrosetta.rosetta.protocols.helical_bundle.BPC_Parameters¶
Bases:
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¶
- property value¶
- class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSampler¶
Bases:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.BackboneGridSamplerHelper¶
Bases:
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:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.BundleGridSamplerHelper¶
Bases:
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:
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.
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
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:
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.
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
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.
set_report_sequence(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) -> None
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.
set_use_threeletter(self: pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilter) -> None
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_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¶
- property value¶
- class pyrosetta.rosetta.protocols.helical_bundle.BundleReporterFilterCreator¶
Bases:
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
- class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelix¶
Bases:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.FitSimpleHelixMultiFunc¶
Bases:
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:
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.
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 &
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_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.
set_use_degrees(self: pyrosetta.rosetta.protocols.helical_bundle.MakeBundle) -> None
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.MakeBundleHelix¶
Bases:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundle¶
Bases:
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_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.
Clears the individual_helix_calculators_ list.
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.helical_bundle.PerturbBundleHelix¶
Bases:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- 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.
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
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