pack

Bindings for core::pack namespace

class pyrosetta.rosetta.core.pack.RTMin

Bases: pybind11_object

__init__(*args, **kwargs)

Overloaded function.

  1. __init__(self: pyrosetta.rosetta.core.pack.RTMin) -> None

  2. __init__(self: pyrosetta.rosetta.core.pack.RTMin, minimize_ligand_chis: bool, minimize_ligand_jumps: bool) -> None

_pybind11_conduit_v1_()
rtmin(self: pyrosetta.rosetta.core.pack.RTMin, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, input_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::RTMin::rtmin(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<class core::pack::task::PackerTask>) const –> void

set_cartesian(self: pyrosetta.rosetta.core.pack.RTMin, cartesian_in: bool) → None

C++: core::pack::RTMin::set_cartesian(bool) –> void

set_nonideal(self: pyrosetta.rosetta.core.pack.RTMin, nonideal_in: bool) → None

C++: core::pack::RTMin::set_nonideal(bool) –> void

pyrosetta.rosetta.core.pack.create_packer_graph(*args, **kwargs)

Overloaded function.

  1. create_packer_graph(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> pyrosetta.rosetta.utility.graph.Graph

C++: core::pack::create_packer_graph(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> class std::shared_ptr<class utility::graph::Graph>

  1. create_packer_graph(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, total_nodes: int, residue_radii: pyrosetta.rosetta.utility.vector1_double) -> pyrosetta.rosetta.utility.graph.Graph

C++: core::pack::create_packer_graph(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long, const class utility::vector1<double, class std::allocator<double> > &) –> class std::shared_ptr<class utility::graph::Graph>

pyrosetta.rosetta.core.pack.figure_out_repackable_residues(pose: pyrosetta.rosetta.core.pose.Pose, to_repack: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, repackable: pyrosetta.rosetta.utility.vector1_bool) → bool

return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb

C++: core::pack::figure_out_repackable_residues(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &, class utility::vector1<bool, class std::allocator<bool> > &) –> bool

pyrosetta.rosetta.core.pack.find_residue_max_radii(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.utility.vector1_double

C++: core::pack::find_residue_max_radii(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> class utility::vector1<double, class std::allocator<double> >

pyrosetta.rosetta.core.pack.get_rotamer_angle_diffs(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t

Get rotamer angle differences

Outer vector is pose length, inner vector is different chi’s

C++: core::pack::get_rotamer_angle_diffs(class core::pose::Pose &, class core::pose::Pose &) –> class utility::vector1<class utility::vector1<double, class std::allocator<double> >, class std::allocator<class utility::vector1<double, class std::allocator<double> > > >

pyrosetta.rosetta.core.pack.make_new_symmetric_PackerTask_by_requested_method(pose: pyrosetta.rosetta.core.pose.Pose, non_symmetric_task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.core.pack.task.PackerTask

C++: core::pack::make_new_symmetric_PackerTask_by_requested_method(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> class std::shared_ptr<class core::pack::task::PackerTask>

pyrosetta.rosetta.core.pack.make_symmetric_PackerTask_by_truncation(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::make_symmetric_PackerTask_by_truncation(const class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.core.pack.make_symmetric_task(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.core.pack.task.PackerTask

Make a task symmetric (Using the logic of PackRotamersMover)

This is robust to being passed a non-symmetric pose

C++: core::pack::make_symmetric_task(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> class std::shared_ptr<class core::pack::task::PackerTask>

pyrosetta.rosetta.core.pack.min_pack(*args, **kwargs)

Overloaded function.

  1. min_pack(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

  2. min_pack(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, cartesian: bool) -> None

  3. min_pack(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, cartesian: bool, nonideal: bool) -> None

Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.

C++: core::pack::min_pack(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool, bool) –> void

pyrosetta.rosetta.core.pack.min_pack_optimize(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, scminmap: core::pack::scmin::SCMinMinimizerMap, mingraph: core::scoring::MinimizationGraph, atc: core::pack::scmin::AtomTreeCollection, min_options: pyrosetta.rosetta.core.optimization.MinimizerOptions, best_state: core::pack::scmin::SidechainStateAssignment) → None

C++: core::pack::min_pack_optimize(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<class core::pack::task::PackerTask>, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>, class std::shared_ptr<class core::pack::scmin::SCMinMinimizerMap>, class std::shared_ptr<class core::scoring::MinimizationGraph>, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>, const class core::optimization::MinimizerOptions &, class core::pack::scmin::SidechainStateAssignment &) –> void

pyrosetta.rosetta.core.pack.min_pack_place_opt_rotamers_on_pose(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, atc: core::pack::scmin::AtomTreeCollection, best_state: core::pack::scmin::SidechainStateAssignment, start_score: float) → None

C++: core::pack::min_pack_place_opt_rotamers_on_pose(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>, const class core::pack::scmin::SidechainStateAssignment &, double) –> void

pyrosetta.rosetta.core.pack.min_pack_setup(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, cartesian: bool, nonideal: bool, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, scminmap: core::pack::scmin::SCMinMinimizerMap, mingraph: core::scoring::MinimizationGraph, atc: core::pack::scmin::AtomTreeCollection, min_options: pyrosetta.rosetta.core.optimization.MinimizerOptions) → None

C++: core::pack::min_pack_setup(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<class core::pack::task::PackerTask>, bool, bool, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets> &, class std::shared_ptr<class core::pack::scmin::SCMinMinimizerMap> &, class std::shared_ptr<class core::scoring::MinimizationGraph> &, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection> &, class std::shared_ptr<class core::optimization::MinimizerOptions> &) –> void

pyrosetta.rosetta.core.pack.off_rotamer_pack(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None
Interface to a version of the packer that uses very little memory

and simultaneously is able to go off rotamer and explore more of sidechain conformation space. Quite a bit faster than the min-packer.

C++: core::pack::off_rotamer_pack(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.core.pack.off_rotamer_pack_optimize(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, rotsets: core::pack::rotamer_set::ContinuousRotamerSets, atc: core::pack::scmin::AtomTreeCollection, ig: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph, best_state: core::pack::scmin::SidechainStateAssignment) → None

C++: core::pack::off_rotamer_pack_optimize(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::rotamer_set::ContinuousRotamerSets &, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>, class core::pack::interaction_graph::SimpleInteractionGraph &, class core::pack::scmin::SidechainStateAssignment &) –> void

pyrosetta.rosetta.core.pack.off_rotamer_pack_setup(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: core::pack::rotamer_set::ContinuousRotamerSets, atc: core::pack::scmin::AtomTreeCollection, ig: pyrosetta.rosetta.core.pack.interaction_graph.SimpleInteractionGraph) → None

C++: core::pack::off_rotamer_pack_setup(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<class core::pack::rotamer_set::ContinuousRotamerSets> &, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection> &, class std::shared_ptr<class core::pack::interaction_graph::SimpleInteractionGraph> &) –> void

pyrosetta.rosetta.core.pack.off_rotamer_pack_update_pose(pose: pyrosetta.rosetta.core.pose.Pose, rotsets: core::pack::rotamer_set::ContinuousRotamerSets, atc: core::pack::scmin::AtomTreeCollection, best_state: core::pack::scmin::SidechainStateAssignment) → None

C++: core::pack::off_rotamer_pack_update_pose(class core::pose::Pose &, const class core::pack::rotamer_set::ContinuousRotamerSets &, class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>, const class core::pack::scmin::SidechainStateAssignment &) –> void

pyrosetta.rosetta.core.pack.optimizeH(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None
This function will optimize the placement of all movable

hydrogen atoms. This includes the hydroxyl hydrogens as well as the HIS protonation state. If the -flip_HNQ flag is on the command line, then it will also consider the flip states of histadine, asparagine and glutamine, (nearly) as described by Word et al. 1999.

C++: core::pack::optimizeH(class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.optimize_H_and_notify(pose: pyrosetta.rosetta.core.pose.Pose, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) → None

Call optimizeH and tell the user what chi angles have changed

C++: core::pack::optimize_H_and_notify(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &) –> void

pyrosetta.rosetta.core.pack.pack_missing_sidechains(*args, **kwargs)

Overloaded function.

  1. pack_missing_sidechains(pose: pyrosetta.rosetta.core.pose.Pose, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) -> None

  2. pack_missing_sidechains(pose: pyrosetta.rosetta.core.pose.Pose, missing: pyrosetta.rosetta.core.id.AtomID_Map_bool_t, threads_to_request: int) -> None

This function runs rotamer trials on residues missing sidechain density (as described

by the AtomID_Mask).

this function will run rotamer trials on sidechains with missing density. It first sets up a PackerTask with repacking freedom for residues with sidechain missing atoms in the missing AtomID_Mask, then runs rotamer_trials. This function is smart enough to ignore missing virtual atoms

In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

C++: core::pack::pack_missing_sidechains(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &, const unsigned long) –> void

pyrosetta.rosetta.core.pack.pack_rotamers(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None
The entry point to calling the packer, which optimizes side-chain identities and conformations

(if you’re designing) or conformations alone (if you’re predicting structures).

Wraps the two very distinct and separate stages of rotamer packing, which are factored so that they may be called asynchronously. Use this wrapper as a base model for higher-level packing routines (such as pack_rotamers_loop).

C++: core::pack::pack_rotamers(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.core.pack.pack_rotamers_cleanup(pose: pyrosetta.rosetta.core.pose.Pose, annealable_graph: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) → None

Provide the opportunity to clean up cached data from the pose or scorefunction after packing.

This should be called after pack_rotamers_run. It is called from the pack_rotamers() function.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::pack_rotamers_cleanup(class core::pose::Pose &, class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase>) –> void

pyrosetta.rosetta.core.pack.pack_rotamers_loop(*args, **kwargs)

Overloaded function.

  1. pack_rotamers_loop(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, nloop: int, results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t) -> None

C++: core::pack::pack_rotamers_loop(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, const unsigned long, class utility::vector1<struct std::pair<double, std::string >, class std::allocator<struct std::pair<double, std::string > > > &) –> void

  1. pack_rotamers_loop(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, nloop: int, results: pyrosetta.rosetta.utility.vector1_std_pair_double_std_string_t, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None

Run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results.

C++: core::pack::pack_rotamers_loop(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, const unsigned long, class utility::vector1<struct std::pair<double, std::string >, class std::allocator<struct std::pair<double, std::string > > > &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

  1. pack_rotamers_loop(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, nloop: int) -> None

C++: core::pack::pack_rotamers_loop(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, const unsigned long) –> void

pyrosetta.rosetta.core.pack.pack_rotamers_run(*args, **kwargs)

Overloaded function.

  1. pack_rotamers_run(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> float

  2. pack_rotamers_run(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, rot_to_pack: pyrosetta.rosetta.utility.vector0_int) -> float

  3. pack_rotamers_run(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) -> float

Run simulated annealing, return the energy of the best rotamer assignment

found, and place the best rotamers onto the input pose.

C++: core::pack::pack_rotamers_run(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::pack::rotamer_set::FixbbRotamerSets>, class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase>, class utility::vector0<int, class std::allocator<int> >, class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> double

  1. pack_rotamers_run(pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, rot_to_pack: pyrosetta.rosetta.utility.vector0_int, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver, bestrotamer_at_seqpos: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, bestenergy: float) -> None

Run simulated annealing and return the best rotamer assignment

found. This function does not modify the input pose.

C++: core::pack::pack_rotamers_run(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::pack::rotamer_set::FixbbRotamerSets>, class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase>, class utility::vector0<int, class std::allocator<int> >, class std::shared_ptr<class core::pack::annealer::AnnealerObserver>, class ObjexxFCL::FArray1D<int> &, float &) –> void

pyrosetta.rosetta.core.pack.pack_rotamers_setup(*args, **kwargs)

Overloaded function.

  1. pack_rotamers_setup(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase) -> None

  2. pack_rotamers_setup(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, ig: pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase, nloop: int) -> None

Get rotamers, compute energies.

In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

C++: core::pack::pack_rotamers_setup(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>, class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase> &, unsigned long) –> void

  1. pack_rotamers_setup(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) -> pyrosetta.rosetta.core.pack.interaction_graph.AnnealableGraphBase

PyRosetta compatible version.

C++: core::pack::pack_rotamers_setup(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>) –> class std::shared_ptr<class core::pack::interaction_graph::AnnealableGraphBase>

pyrosetta.rosetta.core.pack.pack_scorefxn_pose_handshake(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::pack_scorefxn_pose_handshake(class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.reinitialize_mingraph_neighborhood_for_residue(pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, bgres: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, scminmap: core::pack::scmin::SCMinMinimizerMap, rsd: pyrosetta.rosetta.core.conformation.Residue, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, mingraph: core::scoring::MinimizationGraph) → None

C++: core::pack::reinitialize_mingraph_neighborhood_for_residue(class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::pack::scmin::SCMinMinimizerMap &, const class core::conformation::Residue &, class basic::datacache::BasicDataCache &, class core::scoring::MinimizationGraph &) –> void

pyrosetta.rosetta.core.pack.repackable_residues(the_task: pyrosetta.rosetta.core.pack.task.PackerTask) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::repackable_residues(const class core::pack::task::PackerTask &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.pack.residue_rotamer_recovery(*args, **kwargs)

Overloaded function.

  1. residue_rotamer_recovery(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> float

  2. residue_rotamer_recovery(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, difference: float) -> float

Percentage of residues which have same rotamers

C++: core::pack::residue_rotamer_recovery(class core::pose::Pose &, class core::pose::Pose &, double) –> double

pyrosetta.rosetta.core.pack.rotamer_recovery(*args, **kwargs)

Overloaded function.

  1. rotamer_recovery(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> float

  2. rotamer_recovery(pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, difference: float) -> float

Percentage of rotamers recovered

C++: core::pack::rotamer_recovery(class core::pose::Pose &, class core::pose::Pose &, double) –> double

pyrosetta.rosetta.core.pack.rotamer_trials(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, input_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::rotamer_trials(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

pyrosetta.rosetta.core.pack.symmetric_rotamer_trials(pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, input_task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::symmetric_rotamer_trials(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void