Rosetta 3.4
Namespaces | Classes | Typedefs | Functions
core::pack Namespace Reference

Namespaces

namespace  annealer
namespace  dunbrack
namespace  interaction_graph
namespace  rotamer_set
namespace  scmin
namespace  task

Classes

class  RTMin

Typedefs

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

Functions

void make_symmetric_PackerTask (pose::Pose const &pose, pack::task::PackerTaskOP 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)
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)
 Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.
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.
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.
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)
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
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
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.
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.
void symmetric_pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP 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.
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.
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.
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 input_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 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().

void core::pack::make_symmetric_PackerTask ( pose::Pose const &  pose,
pack::task::PackerTaskOP  task 
)
void core::pack::min_pack ( pose::Pose pose,
scoring::ScoreFunction const &  sfxn,
task::PackerTaskCOP  input_task 
)
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(), and core::import_pose::build_pose_as_is2().

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::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::apply(), protocols::simple_moves::RepackSidechainsMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::seeded_abinitio::SeedSetupMover::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::abinitio::DomainAssembly::apply(), protocols::simple_moves::ddG::calculate(), protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::protein_interface_design::AlaScan::ddG_for_single_residue(), 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::protein_interface_design::AlaScan::report_symmetry(), protocols::forge::methods::restore_residues(), and protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile().

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 
)

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(), and protocols::simple_moves::PackRotamersMover::setup().

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  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  input_task 
)
static basic::Tracer core::pack::TR ( "core.pack.rotamer_trials"  ) [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.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]
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