pack

Bindings for core::pack namespace

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

This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask)

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

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_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, class std::basic_string<char> >, class std::allocator<struct std::pair<double, class std::basic_string<char> > > > &) –> 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

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, class std::basic_string<char> >, class std::allocator<struct std::pair<double, class std::basic_string<char> > > > &, 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
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> >) –> 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, bestrotamer_at_seqpos: ObjexxFCL::FArray1D<int>, 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 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

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> &) –> 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

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