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Rosetta
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pack rotamers module More...
#include <core/pack/pack_rotamers.hh>#include <core/pack/packer_neighbors.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/make_symmetric_task.hh>#include <core/pack/rotamer_set/RotamerSet.hh>#include <core/pack/rotamer_set/RotamerSets.hh>#include <core/pack/rotamer_set/symmetry/SymmetricRotamerSets.hh>#include <core/pack/annealer/AnnealerFactory.hh>#include <core/pack/annealer/SimAnnealerBase.hh>#include <core/pack/interaction_graph/InteractionGraphFactory.hh>#include <core/pack/interaction_graph/AnnealableGraphBase.hh>#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>#include <core/pose/symmetry/util.hh>#include <core/conformation/Residue.hh>#include <utility/graph/Graph.fwd.hh>#include <core/pose/Pose.hh>#include <core/scoring/ScoreFunction.hh>#include <basic/prof.hh>#include <basic/Tracer.hh>#include <ObjexxFCL/format.hh>#include <basic/options/keys/packing.OptionKeys.gen.hh>#include <utility/thread/backwards_thread_local.hh>#include <utility/vector0.hh>#include <utility/vector1.hh>#include <ObjexxFCL/FArray1D.hh>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::pack | |
Functions | |
| static basic::Tracer | core::pack::tt ("core.pack.pack_rotamers", basic::t_info) |
| void | core::pack::pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task) |
| 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). More... | |
| void | core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop) |
| void | core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results) |
| void | core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > &pose_list) |
| Run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results. More... | |
| void | core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets, interaction_graph::AnnealableGraphBaseOP &ig, core::Size const nloop) |
| Get rotamers, compute energies. More... | |
| interaction_graph::AnnealableGraphBaseOP | core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets) |
| PyRosetta compatible version. More... | |
| Real | core::pack::pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::AnnealableGraphBaseOP ig, utility::vector0< int > rot_to_pack=utility::vector0< int >(), annealer::AnnealerObserverOP observer=nullptr) |
| Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose. More... | |
| void | core::pack::pack_rotamers_run (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::AnnealableGraphBaseOP ig, utility::vector0< int > rot_to_pack, annealer::AnnealerObserverOP observer, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy) |
| Runs simulated annealing and returns the best identified rotamers and energies. More... | |
| void | core::pack::pack_rotamers_cleanup (core::pose::Pose &pose, core::pack::interaction_graph::AnnealableGraphBaseOP annealable_graph) |
| Provide the opportunity to clean up cached data from the pose or scorefunction after packing. More... | |
pack rotamers module
1.9.1