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core::pack Namespace Reference

Namespaces

 annealer
 
 dunbrack
 
 guidance_scoreterms
 
 hbonds
 
 interaction_graph
 
 palette
 
 rotamer_set
 
 rotamers
 
 scmin
 
 task
 

Classes

class  RTMin
 

Typedefs

using SymmetricConformation = conformation::symmetry::SymmetricConformation
 
using SymmetryInfo = conformation::symmetry::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)
 
task::PackerTaskOP make_symmetric_task (pose::Pose const &pose, task::PackerTaskCOP task)
 Make a task symmetric (Using the logic of PackRotamersMover) More...
 
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)
 
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, utility::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_off_rotamer_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 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 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 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 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 assign_random_continuous_rotamer (rotamer_set::ContinuousRotamerSet const &rotset, scmin::ResidueAtomTreeCollection &resatc, Size ranrot_on_moltenres)
 
void 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 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 off_rotamer_pack_update_pose (pose::Pose &pose, rotamer_set::ContinuousRotamerSets const &rotsets, scmin::AtomTreeCollectionOP atc, scmin::SidechainStateAssignment const &best_state)
 
void 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...
 
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 (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). 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)
 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 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)
 Run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results. More...
 
void 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 pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets)
 PyRosetta compatible version. More...
 
Real 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 >())
 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::AnnealableGraphBaseOP ig, utility::vector0< int > rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy)
 Runs simulated annealing and returns the best identified rotamers and energies. More...
 
void 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...
 
utility::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...
 
utility::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 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 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, basic::datacache::BasicDataCache &res_data_cache, scoring::MinimizationGraph &mingraph)
 
static basic::Tracer TR ("core.pack.util")
 
core::Real residue_rotamer_recovery (Pose &pose, Pose &ref_pose, core::Real difference)
 Percentage of residues which have same rotamers. More...
 
core::Real rotamer_recovery (Pose &pose, Pose &ref_pose, core::Real difference)
 Percentage of rotamers recovered. More...
 
utility::vector1
< utility::vector1< Real > > 
get_rotamer_angle_diffs (Pose &pose, Pose &ref_pose)
 Get rotamer angle differences. More...
 

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 &  curr_pose,
pose::Pose const &  alt_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,
utility::graph::Graph const &  packer_neighbor_graph,
scmin::SCMinMinimizerMap const &  sc_min_map 
)
utility::graph::GraphOP core::pack::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.

References find_residue_max_radii(), and core::pose::Pose::size().

Referenced by protocols::RotamerDump::RotamerDumpMover::apply(), protocols::minimization_packing::BoltzmannRotamerMover::apply(), protocols::simple_filters::PackerNeighborGraphFilter::apply(), protocols::simple_moves::ExplicitWaterMover::attach_rotamer_clouds_to_pose_and_rotset(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::motifs::Motif::build_rotamers(), protocols::motifs::build_rotamers_lite(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(), protocols::minimization_packing::GreenPacker::create_fresh_packer_neighbor_graph(), core::pack::hbonds::create_init_and_create_edges_for_hbond_graph(), protocols::minimization_packing::GreenPacker::create_reference_packer_neighbor_graph(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), core::pack::task::residue_selector::find_clashing_shell(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexpack_neighbor_graph(), protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), core::pack::interaction_graph::SimpleInteractionGraph::initialize(), min_pack_setup(), off_rotamer_pack_setup(), pack_rotamers_setup(), rotamer_trials(), core::pack::RTMin::rtmin(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::rotamer_recovery::RRProtocolRTMin::run(), protocols::hbnet::HBNet::run(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), and symmetric_rotamer_trials().

utility::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::size(), and TR().

Referenced by protocols::minimization_packing::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::size().

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 
)
utility::vector1< utility::vector1< Real > > core::pack::get_rotamer_angle_diffs ( Pose pose,
Pose ref_pose 
)
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_optimize().

utility::vector1< Real > core::pack::initialize_temperatures_off_rotamer_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 
)
task::PackerTaskOP core::pack::make_symmetric_task ( pose::Pose const &  pose,
task::PackerTaskCOP  task 
)
void core::pack::min_pack ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn,
task::PackerTaskCOP  input_task,
bool  cartesian,
bool  nonideal 
)
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::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 
)
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 
)
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.

References off_rotamer_pack_optimize(), off_rotamer_pack_setup(), off_rotamer_pack_update_pose(), and TR().

Referenced by protocols::minimization_packing::MinPackMover::apply().

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_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_update_pose ( pose::Pose pose,
rotamer_set::ContinuousRotamerSets const &  rotsets,
scmin::AtomTreeCollectionOP  atc,
scmin::SidechainStateAssignment const &  best_state 
)
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

Note
In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

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

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

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).

Wraps the two very distinct and separate stages of rotamer packing, which are factored so that they may be called asynchronously. Use this wrapper as a base model for higher-level packing routines (such as pack_rotamers_loop).

Note
In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

Wraps the two very distinct and separate stages of rotamer packing, which are factored so that they may be called asynchronously. Use this wrapper as a base model for higher-level packing routines (such as pack_rotamers_loop).

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

Referenced by protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_pose(), protocols::hotspot_hashing::HotspotStubSet::add_hotspot_constraints_to_wholepose(), 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::simple_filters::SAXSScoreFilter::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::minimization_packing::RepackSidechainsMover::apply(), protocols::loops::loop_mover::refine::RepackTrial::apply(), protocols::hybridization::CartesianHybridize::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::membrane::MPMutateRelaxMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::backrub(), protocols::minimization_packing::DisulfideOptimizationMover::break_repack_reform(), protocols::simple_ddg::ddG::calculate(), protocols::ddg::ddGMover::calculate_interface_unbound_energy(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_ddg::AlaScan::ddG_for_single_residue(), protocols::simple_ddg::DdGScan::ddG_for_single_residue(), protocols::loop_modeling::refiners::RepackingRefiner::do_apply(), protocols::stepwise::modeler::packer::StepWisePacker::do_packing(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::final_exact_scmin(), protocols::protein_interface_design::movers::finalize_stub_set(), protocols::ligand_docking::ga_ligand_dock::GALigandDock::idealize_and_repack_pose(), protocols::ddg::ddGMover::minimize_with_constraints(), protocols::motifs::mutate_loops_for_search(), protocols::motifs::mutate_position_vector_for_search(), protocols::relax::LocalRelax::optimization_loop(), 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::point_mutation(), core::util::rebuild_disulfide(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::relax::RangeRelaxMover::repack_all(), protocols::relax::RangeRelaxMover::repack_sequence_window(), protocols::relax::RangeRelaxMover::repack_spherical_range(), protocols::simple_ddg::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_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.

This should be called after pack_rotamers_run. It is called from the pack_rotamers() function.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by protocols::minimization_packing::PackRotamersMover::cleanup(), protocols::minimization_packing::GreenPacker::cleanup(), protocols::RotamerDump::RotamerDumpMover::get_annealer_pick_table(), pack_rotamers(), and pack_rotamers_loop().

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

run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results.

Note
In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

References pack_rotamers_loop().

Referenced by protocols::hydrate::Hydrate::apply(), protocols::ddg::ddGMover::apply(), protocols::ddg::ddGMover::relax_wildtype_structure(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().

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 
)

run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results

Note
In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

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 
)

Run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results.

Note
In multi-threaded builds, this function takes an extra parameter for the number of threads to request, for parallel interaction graph precomputation.

References core::chemical::element::F, core::chemical::element::I, core::conformation::Residue::name1(), pack_rotamers_cleanup(), pack_rotamers_run(), pack_rotamers_setup(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), and tt().

Referenced by pack_rotamers_loop().

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 
)
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,
ObjexxFCL::FArray1D_int &  bestrotamer_at_seqpos,
core::PackerEnergy bestenergy 
)

Runs simulated annealing and returns the best identified rotamers and energies.

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

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

Referenced by pack_rotamers(), pack_rotamers_loop(), and pack_rotamers_run().

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 
)
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.

Referenced by pack_rotamers(), and pack_rotamers_loop().

void core::pack::pack_scorefxn_pose_handshake ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn 
)
bool core::pack::pass_metropolis ( Real  temperature,
Real  deltaE 
)
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,
basic::datacache::BasicDataCache &  res_data_cache,
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)
core::Real core::pack::residue_rotamer_recovery ( Pose pose,
Pose ref_pose,
core::Real  difference 
)

Percentage of residues which have same rotamers.

References get_rotamer_angle_diffs(), core::pose::nres_protein(), and TR().

core::Real core::pack::rotamer_recovery ( Pose pose,
Pose ref_pose,
core::Real  difference 
)
void core::pack::rotamer_trials ( pose::Pose pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  input_task 
)

References protocols::mean_field::arg_min(), create_packer_graph(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::pose::symmetry::is_symmetric(), pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), protocols::rigid::random, repackable_residues(), core::pose::Pose::replace_residue(), core::scoring::rg, core::scoring::ScoreFunction::setup_for_packing(), symmetric_rotamer_trials(), TR(), core::scoring::ScoreFunction::update_residue_for_packing(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), protocols::loop_modeling::refiners::RotamerTrialsRefiner::do_apply(), protocols::stepwise::modeler::packer::StepWisePacker::do_packing(), protocols::rna::denovo::movers::RNA_Minimizer::o2prime_trials(), protocols::stepwise::modeler::rna::o2prime_trials(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), and protocols::stepwise::modeler::rna::o2prime::O2PrimePacker::sample_o2prime_hydrogen().

utility::vector1< conformation::ResidueCOP > core::pack::setup_bgres_cops ( pose::Pose const &  pose,
task::PackerTask const &  task 
)
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.pack.util"  )
static
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.rtmin"  )
static
static basic::Tracer core::pack::TR ( "core.pack.min_pack"  ,
basic::t_info   
)
static
static basic::Tracer core::pack::tt ( "core.pack.pack_rotamers"  ,
basic::t_info   
)
static