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core::pack Namespace Reference

Namespaces

 annealer
 
 dunbrack
 
 interaction_graph
 
 rotamer_set
 
 scmin
 
 task
 

Classes

class  RTMin
 

Typedefs

typedef
conformation::symmetry::SymmetricConformation 
SymmetricConformation
 
typedef
conformation::symmetry::SymmetryInfo 
SymmetryInfo
 

Functions

void make_symmetric_PackerTask_by_truncation (pose::Pose const &pose, pack::task::PackerTaskOP task)
 
task::PackerTaskOP make_new_symmetric_PackerTask_by_truncation (pose::Pose const &pose, task::PackerTaskCOP non_symmetric_task)
 
task::PackerTaskOP make_new_symmetric_PackerTask_by_union (pose::Pose const &pose, task::PackerTaskCOP non_symmetric_task)
 
task::PackerTaskOP make_new_symmetric_PackerTask_by_intersection (pose::Pose const &pose, task::PackerTaskCOP non_symmetric_task)
 
task::PackerTaskOP make_new_symmetric_PackerTask_by_requested_method (pose::Pose const &pose, task::PackerTaskCOP non_symmetric_task)
 
void compare_mingraph_and_energy_graph (Size resid, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph const &mingraph)
 
static basic::Tracer TR ("core.pack.min_pack", basic::t_info)
 
static
numeric::random::RandomGenerator 
RG (22307)
 
scmin::SCMinMinimizerMapOP create_scmin_minimizer_map (pose::Pose const &pose, task::PackerTaskCOP task, bool cartesian)
 
scoring::MinimizationGraphOP 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
setup_bgres_cops (pose::Pose const &pose, task::PackerTask const &task)
 
utility::vector1< Realinitialize_temperatures ()
 
utility::vector1< Realinitialize_temperatures_stochastic_pack ()
 
Real 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 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 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 pass_metropolis (Real temperature, Real deltaE)
 
Size n_inner_iterations (Real, Size nrotamers)
 
void 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 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 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 assign_random_continuous_rotamer (rotamer_set::ContinuousRotamerSet const &rotset, scmin::ResidueAtomTreeCollection &resatc, Size ranrot_on_moltenres)
 
void stochastic_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task)
 
static basic::Tracer TR ("core.io.pdb.file_data")
 
void optimize_H_and_notify (pose::Pose &pose, id::AtomID_Mask const &missing)
 Call optimizeH and tell the user what chi angles have changed. More...
 
void optimizeH (pose::Pose &pose, scoring::ScoreFunction const &sfxn)
 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. More...
 
void pack_missing_sidechains (pose::Pose &pose, id::AtomID_Mask const &missing)
 This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask) More...
 
bool figure_out_repackable_residues (core::pose::Pose &pose, core::id::AtomID_Mask const &to_repack, utility::vector1_bool &repackable)
 return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb More...
 
static basic::Tracer tt ("core.pack.pack_rotamers", basic::t_info)
 
void pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task)
 
void pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop)
 
void 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 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)
 
void pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets, interaction_graph::InteractionGraphBaseOP &ig)
 
void setup_IG_res_res_weights (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::RotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig)
 upweights certain edges in the interaction graph if this is specified in the task More...
 
Real pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack=utility::vector0< int >())
 Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose. More...
 
void pack_rotamers_run (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy)
 Runs simulated annealing and returns the. More...
 
void symmetric_pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP non_symmetric_task)
 
void symmetric_pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsOP rotsets, interaction_graph::InteractionGraphBaseOP &ig)
 
Real symmetric_pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack)
 
graph::GraphOP create_packer_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task)
 Constructs a graph where edges represent the possibility of interactions between residue pairs. More...
 
graph::GraphOP create_packer_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, core::Size total_nodes, utility::vector1< Distance > const &residue_radii)
 Constructs a graph where edges represent the possibility of interactions between residue pairs. More...
 
utility::vector1< Distancefind_residue_max_radii (pose::Pose const &pose, task::PackerTaskCOP the_task)
 for each residue in the protein, finds the largest bounding sphere over all allowable rotameric/chemical modifications possible given the input task. More...
 
void pack_scorefxn_pose_handshake (pose::Pose &pose, scoring::ScoreFunction const &scfxn)
 
static
numeric::random::RandomGenerator 
rottrials_RG (10801)
 
static basic::Tracer TR ("core.pack.rotamer_trials")
 
utility::vector1< uintsymmetric_repackable_residues (task::PackerTask const &the_task, pose::Pose &pose)
 
void rotamer_trials (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP input_task)
 
utility::vector1< uintrepackable_residues (task::PackerTask const &the_task)
 
void symmetric_rotamer_trials (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP non_symmetric_task)
 
static
numeric::random::RandomGenerator 
rtmin_RG (206025)
 
static basic::Tracer TR ("core.pack.rtmin")
 
utility::vector1< uintrepackable_residues_dup (task::PackerTask const &the_task)
 
void reinitialize_mingraph_neighborhood_for_residue (pose::Pose &pose, scoring::ScoreFunction const &scorefxn, utility::vector1< conformation::ResidueCOP > const &bgres, pack::scmin::SCMinMinimizerMap const &scminmap, conformation::Residue const &rsd, scoring::MinimizationGraph &mingraph)
 

Typedef Documentation

Function Documentation

Size core::pack::assign_random_continuous_rotamer ( rotamer_set::ContinuousRotamerSet const &  rotset,
scmin::ResidueAtomTreeCollection &  resatc,
Size  ranrot_on_moltenres 
)
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::compare_mingraph_and_energy_graph ( Size  resid,
pose::Pose const &  pose,
scoring::ScoreFunction const &  sfxn,
scoring::MinimizationGraph const &  mingraph 
)
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 
)
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 
)
graph::GraphOP core::pack::create_packer_graph ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task 
)
graph::GraphOP core::pack::create_packer_graph ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task,
core::Size  total_nodes,
utility::vector1< Distance > const &  residue_radii 
)
scmin::SCMinMinimizerMapOP core::pack::create_scmin_minimizer_map ( pose::Pose const &  pose,
task::PackerTaskCOP  task,
bool  cartesian 
)
bool core::pack::figure_out_repackable_residues ( core::pose::Pose pose,
core::id::AtomID_Mask const &  to_repack,
utility::vector1_bool &  repackable 
)

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

References core::id::AtomID_Map< T >::get(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and TR().

Referenced by protocols::simple_moves::RepackSidechainsMover::apply(), and pack_missing_sidechains().

utility::vector1< Distance > core::pack::find_residue_max_radii ( pose::Pose const &  pose,
task::PackerTaskCOP  the_task 
)

for each residue in the protein, finds the largest bounding sphere over all allowable rotameric/chemical modifications possible given the input task.

References core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by create_packer_graph(), and protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexpack_neighbor_graph().

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 
)
utility::vector1< Real > core::pack::initialize_temperatures ( )

Referenced by min_pack().

utility::vector1< Real > core::pack::initialize_temperatures_stochastic_pack ( )

Referenced by stochastic_pack().

task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_intersection ( pose::Pose const &  pose,
task::PackerTaskCOP  non_symmetric_task 
)
task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_requested_method ( pose::Pose const &  pose,
task::PackerTaskCOP  non_symmetric_task 
)
task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_truncation ( pose::Pose const &  pose,
task::PackerTaskCOP  non_symmetric_task 
)
task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_union ( pose::Pose const &  pose,
task::PackerTaskCOP  non_symmetric_task 
)
void core::pack::make_symmetric_PackerTask_by_truncation ( pose::Pose const &  pose,
pack::task::PackerTaskOP  task 
)
void core::pack::min_pack ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn,
task::PackerTaskCOP  input_task,
bool  cartesian,
bool  nonideal 
)
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 
)
Size core::pack::n_inner_iterations ( Real  ,
Size  nrotamers 
)

Referenced by min_pack(), and stochastic_pack().

void core::pack::optimize_H_and_notify ( pose::Pose pose,
id::AtomID_Mask const &  missing 
)
void core::pack::optimizeH ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn 
)

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.

References pack_rotamers().

Referenced by optimize_H_and_notify().

void core::pack::pack_missing_sidechains ( core::pose::Pose pose,
core::id::AtomID_Mask const &  missing 
)

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

References core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), figure_out_repackable_residues(), and pack_rotamers().

Referenced by protocols::comparative_modeling::ThreadingMover::apply(), core::import_pose::build_pose_as_is2(), and core::import_pose::ImportPoseOptions::init_from_options().

void core::pack::pack_rotamers ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task 
)

References core::pose::symmetry::is_symmetric(), pack_rotamers_run(), pack_rotamers_setup(), pack_scorefxn_pose_handshake(), and symmetric_pack_rotamers().

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::protein_interface_design::movers::PlaceOnLoop::ala_pose_loop(), protocols::seeded_abinitio::SeedSetupMover::apply(), protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::simple_moves::RepackSidechainsMover::apply(), protocols::loops::loop_mover::refine::RepackTrial::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::swa::protein::StepWiseProteinPacker::apply_regular_packer(), protocols::swa::protein::StepWiseProteinResidueSampler::apply_regular_packer(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::simple_moves::ddG::calculate(), protocols::ddg::ddGMover::calculate_interface_unbound_energy(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::motifs::mutate_loops_for_search(), optimizeH(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states(), pack_missing_sidechains(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::pair_sets_with_positions(), protocols::protein_interface_design::movers::PlaceStubMover::parse_my_tag(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::parse_my_tag(), protocols::protein_interface_design::movers::parse_stub_sets(), point_mutation(), core::util::rebuild_disulfide(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::forge::methods::restore_residues(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::rotamer_recovery::RRProtocolPackRotamers::run(), and protocols::docking::DockMCMCycle::setup_protocol().

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 
)

References pack_rotamers_loop().

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 
)
Real core::pack::pack_rotamers_run ( pose::Pose pose,
task::PackerTaskCOP  task,
rotamer_set::FixbbRotamerSetsCOP  rotsets,
interaction_graph::InteractionGraphBaseOP  ig,
utility::vector0< int rot_to_pack 
)
void core::pack::pack_rotamers_run ( pose::Pose const &  pose,
task::PackerTaskCOP  task,
rotamer_set::FixbbRotamerSetsCOP  rotsets,
interaction_graph::InteractionGraphBaseOP  ig,
utility::vector0< int rot_to_pack,
ObjexxFCL::FArray1D_int &  bestrotamer_at_seqpos,
core::PackerEnergy bestenergy 
)

Runs simulated annealing and returns the.

Run simulated annealing and return the best rotamer assignment found. This function does not modify the input pose.

References core::pose::Pose::total_residue().

void core::pack::pack_rotamers_setup ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task,
rotamer_set::RotamerSetsOP  rotsets,
interaction_graph::InteractionGraphBaseOP &  ig 
)
void core::pack::pack_scorefxn_pose_handshake ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn 
)
bool core::pack::pass_metropolis ( Real  temperature,
Real  deltaE 
)

References RG().

Referenced by min_pack(), and stochastic_pack().

void core::pack::reinitialize_mingraph_neighborhood_for_residue ( pose::Pose pose,
scoring::ScoreFunction const &  scorefxn,
utility::vector1< conformation::ResidueCOP > const &  bgres,
pack::scmin::SCMinMinimizerMap const &  scminmap,
conformation::Residue const &  rsd,
scoring::MinimizationGraph &  mingraph 
)
utility::vector1< uint > core::pack::repackable_residues ( task::PackerTask const &  the_task)
utility::vector1< uint > core::pack::repackable_residues_dup ( task::PackerTask const &  the_task)
static numeric::random::RandomGenerator core::pack::RG ( 22307  )
static
void core::pack::rotamer_trials ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  input_task 
)
static numeric::random::RandomGenerator core::pack::rottrials_RG ( 10801  )
static
static numeric::random::RandomGenerator core::pack::rtmin_RG ( 206025  )
static
utility::vector1< conformation::ResidueCOP > core::pack::setup_bgres_cops ( pose::Pose const &  pose,
task::PackerTask const &  task 
)
void core::pack::setup_IG_res_res_weights ( pose::Pose const &  pose,
task::PackerTaskCOP  task,
rotamer_set::RotamerSetsCOP  rotsets,
interaction_graph::InteractionGraphBaseOP  ig 
)
void core::pack::stochastic_pack ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn,
task::PackerTaskCOP  task 
)
void core::pack::symmetric_pack_rotamers ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  non_symmetric_task 
)
Real core::pack::symmetric_pack_rotamers_run ( pose::Pose pose,
task::PackerTaskCOP  task,
rotamer_set::symmetry::SymmetricRotamerSetsCOP  rotsets,
interaction_graph::InteractionGraphBaseOP  ig,
utility::vector0< int rot_to_pack 
)
void core::pack::symmetric_pack_rotamers_setup ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task,
rotamer_set::symmetry::SymmetricRotamerSetsOP  rotsets,
interaction_graph::InteractionGraphBaseOP &  ig 
)
utility::vector1< uint > core::pack::symmetric_repackable_residues ( task::PackerTask const &  the_task,
pose::Pose pose 
)
void core::pack::symmetric_rotamer_trials ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  non_symmetric_task 
)
static basic::Tracer core::pack::TR ( "core.io.pdb.file_data"  )
static

Tracer instance for this file Named after the original location of this code

static basic::Tracer core::pack::TR ( "core.pack.rotamer_trials"  )
static
static basic::Tracer core::pack::TR ( "core.pack.min_pack"  ,
basic::t_info   
)
static
static basic::Tracer core::pack::TR ( "core.pack.rtmin"  )
static
static basic::Tracer core::pack::tt ( "core.pack.pack_rotamers"  ,
basic::t_info   
)
static