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Rosetta
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pack rotamers with minimization module More...
#include <core/pack/min_pack.hh>#include <core/pack/rtmin.hh>#include <core/pack/packer_neighbors.hh>#include <core/pack/scmin/AtomTreeCollection.hh>#include <core/pack/scmin/SCMinMinimizerMap.hh>#include <core/pack/scmin/AtomTreeSCMinMinimizerMap.hh>#include <core/pack/scmin/CartSCMinMinimizerMap.hh>#include <core/pack/scmin/SidechainStateAssignment.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/rotamer_set/ContinuousRotamerSet.hh>#include <core/pack/rotamer_set/RotamerSet.hh>#include <core/pack/rotamer_set/RotamerSets.hh>#include <core/pack/interaction_graph/SimpleInteractionGraph.hh>#include <core/pack/interaction_graph/NPDHBSimpleInteractionGraph.hh>#include <core/conformation/Residue.hh>#include <utility/graph/Graph.hh>#include <core/pose/Pose.hh>#include <core/scoring/Energies.hh>#include <core/scoring/EnergyMap.hh>#include <core/scoring/EnergyGraph.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreType.hh>#include <core/scoring/MinimizationGraph.hh>#include <core/scoring/methods/LongRangeTwoBodyEnergy.hh>#include <core/scoring/LREnergyContainer.hh>#include <core/optimization/Minimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <basic/Tracer.hh>#include <numeric/random/random.hh>#include <basic/options/option.hh>#include <basic/options/keys/packing.OptionKeys.gen.hh>#include <core/pack/dunbrack/DunbrackRotamer.hh>#include <utility/vector1.hh>#include <utility/thread/backwards_thread_local.hh>Namespaces | |
| core | |
| A class for reading in the atom type properties. | |
| core::pack | |
Functions | |
| void | core::pack::compare_mingraph_and_energy_graph (Size resid, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph const &mingraph) |
| static basic::Tracer | core::pack::TR ("core.pack.min_pack", basic::t_info) |
| scmin::SCMinMinimizerMapOP | core::pack::create_scmin_minimizer_map (pose::Pose const &pose, task::PackerTaskCOP task, bool cartesian) |
| scoring::MinimizationGraphOP | core::pack::create_minimization_graph (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::Graph const &packer_neighbor_graph, scmin::SCMinMinimizerMap const &sc_min_map) |
| utility::vector1< conformation::ResidueCOP > | core::pack::setup_bgres_cops (pose::Pose const &pose, task::PackerTask const &task) |
| utility::vector1< Real > | core::pack::initialize_temperatures () |
| utility::vector1< Real > | core::pack::initialize_temperatures_off_rotamer_pack () |
| Real | core::pack::get_residue_current_energy (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets, Size resid, Size moltenres_id) |
| Real | core::pack::get_total_energy_for_state (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets) |
| Real | core::pack::minimize_alt_rotamer (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, optimization::MinimizerOptions const &min_options, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets, Size resid, Size moltenres_id, Size rotamer_state_on_moltenres) |
| bool | core::pack::pass_metropolis (Real temperature, Real deltaE) |
| Size | core::pack::n_inner_iterations (Real, Size nrotamers) |
| void | core::pack::assign_random_rotamers (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraphOP mingraph, scmin::SCMinMinimizerMapOP scminmap, optimization::MinimizerOptions const &min_options, scmin::SidechainStateAssignment &curr_state, scmin::SidechainStateAssignment &best_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSetsCOP rotsets) |
| void | core::pack::min_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task, bool cartesian=false, bool nonideal=false) |
| Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm. More... | |
| void | core::pack::min_pack_setup (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTaskOP task, bool cartesian, bool nonideal, rotamer_set::RotamerSetsOP &rotsets, scmin::SCMinMinimizerMapOP &scminmap, scoring::MinimizationGraphOP &mingraph, scmin::AtomTreeCollectionOP &atc, optimization::MinimizerOptionsOP &min_options) |
| void | core::pack::min_pack_optimize (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTaskOP task, rotamer_set::RotamerSetsOP rotsets, scmin::SCMinMinimizerMapOP scminmap, scoring::MinimizationGraphOP mingraph, scmin::AtomTreeCollectionOP atc, optimization::MinimizerOptions const &min_options, scmin::SidechainStateAssignment &best_state) |
| void | core::pack::min_pack_place_opt_rotamers_on_pose (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, rotamer_set::RotamerSetsOP rotsets, scmin::AtomTreeCollectionOP atc, scmin::SidechainStateAssignment const &best_state, Real start_score) |
| void | core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph (Size resid, pose::Pose const &curr_pose, pose::Pose const &alt_pose, scoring::ScoreFunction const &sfxn, interaction_graph::SimpleInteractionGraph const &ig) |
| Size | core::pack::assign_random_continuous_rotamer (rotamer_set::ContinuousRotamerSet const &rotset, scmin::ResidueAtomTreeCollection &resatc, Size ranrot_on_moltenres) |
| void | core::pack::off_rotamer_pack_setup (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task, rotamer_set::ContinuousRotamerSetsOP &rotsets, scmin::AtomTreeCollectionOP &atc, interaction_graph::SimpleInteractionGraphOP &ig) |
| void | core::pack::off_rotamer_pack_optimize (pose::Pose const &, scoring::ScoreFunction const &, rotamer_set::ContinuousRotamerSets const &rotsets, scmin::AtomTreeCollectionOP atc, interaction_graph::SimpleInteractionGraph &ig, scmin::SidechainStateAssignment &best_state) |
| void | core::pack::off_rotamer_pack_update_pose (pose::Pose &pose, rotamer_set::ContinuousRotamerSets const &rotsets, scmin::AtomTreeCollectionOP atc, scmin::SidechainStateAssignment const &best_state) |
| void | core::pack::off_rotamer_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task) |
| 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. More... | |
pack rotamers with minimization module
1.9.1