Rosetta Core  2014.35
Namespaces | Functions | Variables
min_pack.cc File Reference

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/conformation/Residue.hh>
#include <core/graph/Graph.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.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>

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)
 
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, 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< Realcore::pack::initialize_temperatures ()
 
utility::vector1< Realcore::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 &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 (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...
 

Variables

static basic::Tracer core::pack::TR ("core.pack.min_pack", basic::t_info)
 
static
numeric::random::RandomGenerator 
core::pack::RG (22307)
 

Detailed Description

pack rotamers with minimization module

Author
Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)