Rosetta Core  2014.35
Namespaces | Classes | Typedefs | Functions | Variables
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)
 
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_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 &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 (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...
 
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...
 
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)
 
interaction_graph::InteractionGraphBaseOP pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets)
 
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)
 
interaction_graph::InteractionGraphBaseOP symmetric_pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsOP rotsets)
 
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)
 
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)
 
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)
 

Variables

static basic::Tracer TR ("core.pack.min_pack", basic::t_info)
 
static
numeric::random::RandomGenerator 
RG (22307)
 
static basic::Tracer TR ("core.io.pdb.file_data")
 
static basic::Tracer tt ("core.pack.pack_rotamers", basic::t_info)
 
static
numeric::random::RandomGenerator 
rottrials_RG (10801)
 
static basic::Tracer TR ("core.pack.rotamer_trials")
 
static
numeric::random::RandomGenerator 
rtmin_RG (206025)
 
static basic::Tracer TR ("core.pack.rtmin")
 

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(), restype, core::pose::Pose::total_residue(), and TR.

Referenced by 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 chemical, core::conformation::Residue::nbr_radius(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by create_packer_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 ( )

References minpack_temp_schedule, option, and user.

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 
)
void core::pack::min_pack ( pose::Pose &  pose,
scoring::ScoreFunction const &  sfxn,
task::PackerTaskCOP  input_task,
bool  cartesian,
bool  nonideal 
)

Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.

References min_pack_optimize(), min_pack_place_opt_rotamers_on_pose(), and min_pack_setup().

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.

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_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 option, and 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(), figure_out_repackable_residues(), core::scoring::get_score_function(), and pack_rotamers().

Referenced by core::import_pose::build_pose_as_is2().

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

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 
)

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 
)

Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose.

References pack_rotamers_run(), core::pose::Pose::replace_residue(), and core::pose::Pose::total_residue().

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 annealer, PROF_START, PROF_STOP, basic::SIMANNEALING, and core::pose::Pose::total_residue().

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

pose and score function must have met before packing may begin; this function will force a score evaluation if the energie's scorefunction-info object does not match that of the given score function.

Referenced by min_pack_setup(), off_rotamer_pack_setup(), pack_rotamers(), pack_rotamers_setup(), rotamer_trials(), symmetric_pack_rotamers(), symmetric_pack_rotamers_setup(), and symmetric_rotamer_trials().

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

upweights certain edges in the interaction graph if this is specified in the task

References core::pack::interaction_graph::EdgeBase::get_other_ind().

Referenced by pack_rotamers_loop().

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 
)
interaction_graph::InteractionGraphBaseOP core::pack::symmetric_pack_rotamers_setup ( pose::Pose &  pose,
scoring::ScoreFunction const &  scfxn,
task::PackerTaskCOP  task,
rotamer_set::symmetry::SymmetricRotamerSetsOP  rotsets 
)

Referenced by symmetric_pack_rotamers().

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 
)

Variable Documentation

numeric::random::RandomGenerator core::pack::RG(22307)
static
numeric::random::RandomGenerator core::pack::rottrials_RG(10801)
static
numeric::random::RandomGenerator core::pack::rtmin_RG(206025)
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

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