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< Real >	initialize_temperatures ()
utility::vector1< Real >	initialize_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 >(), annealer::AnnealerObserverOP observer=nullptr)
	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, annealer::AnnealerObserverOP observer, 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< Distance >	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. More...
void	pack_scorefxn_pose_handshake (pose::Pose &pose, scoring::ScoreFunction const &scfxn)
static basic::Tracer	TR ("core.pack.rotamer_trials")
utility::vector1< uint >	symmetric_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< uint >	repackable_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< uint >	repackable_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

SymmetricConformation

using core::pack::SymmetricConformation = typedef conformation::symmetry::SymmetricConformation

SymmetryInfo

using core::pack::SymmetryInfo = typedef conformation::symmetry::SymmetryInfo

Function Documentation

assign_random_continuous_rotamer()

Size core::pack::assign_random_continuous_rotamer	(	rotamer_set::ContinuousRotamerSet const &	rotset,
		scmin::ResidueAtomTreeCollection &	resatc,
		Size	ranrot_on_moltenres
	)

Returns the rotamer index (1 for the current rotamer) for a randomly assigned rotamer

References core::pack::rotamer_set::ContinuousRotamerSet::baserotamer_data(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_mean(), core::pack::dunbrack::DunbrackRotamerSampleData::chi_sd(), core::pack::rotamer_set::ContinuousRotamerSet::current_rotamer_coords(), core::pack::rotamer_set::ContinuousRotamerSet::get_n_baserotamers_for_rotblock(), core::pack::rotamer_set::ContinuousRotamerSet::get_rotblock_index_for_sampling_rotamer(), core::pack::dunbrack::DunbrackRotamerSampleData::nchi(), core::pack::rotamer_set::ContinuousRotamerSet::pick_baserotamer_from_rotblock(), core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock(), core::scoring::rg, core::pack::rotamer_set::ContinuousRotamerSet::sampling_id_for_current_rotamer(), core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(), core::pack::scmin::ResidueAtomTreeCollection::set_chi(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().

Referenced by off_rotamer_pack_optimize().

assign_random_rotamers()

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
	)

References core::pack::scmin::SidechainStateAssignment::assign_energy(), core::pack::scmin::SidechainStateAssignment::assign_state(), compare_mingraph_and_energy_graph(), get_total_energy_for_state(), minimize_alt_rotamer(), core::scoring::rg, core::pack::scmin::SidechainStateAssignment::state_momento(), and core::scoring::ScoreFunction::weights().

Referenced by min_pack_optimize().

compare_mingraph_and_energy_graph()

void core::pack::compare_mingraph_and_energy_graph	(	Size	resid,
		pose::Pose const &	pose,
		scoring::ScoreFunction const &	sfxn,
		scoring::MinimizationGraph const &	mingraph
	)

References core::scoring::EMapVector::dot(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::eval_res_onebody_energies_for_minnode(), core::scoring::eval_res_pair_energy_for_minedge(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::fa_sol, core::scoring::MinimizationGraph::get_minimization_node(), core::scoring::hbond_bb_sc, core::scoring::Energies::onebody_energies(), core::pose::Pose::residue(), core::scoring::EMapVector::show_if_nonzero_weight(), core::id::to_string(), core::scoring::total_score, TR(), core::scoring::Energies::weights(), and core::scoring::ScoreFunction::weights().

Referenced by assign_random_rotamers(), get_residue_current_energy(), min_pack_optimize(), and core::pack::RTMin::rtmin().

compare_simple_inteaction_graph_alt_state_and_energy_graph()

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
	)

References core::scoring::EMapVector::dot(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::pack::interaction_graph::SimpleNode::get_alternate(), core::pack::interaction_graph::SimpleNode::get_current(), core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node(), core::conformation::Residue::natoms(), core::scoring::Energies::onebody_energies(), core::pack::interaction_graph::SimpleNode::proposed_one_body_energy(), core::pose::Pose::residue(), core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::EMapVector::show_weighted(), core::pose::Pose::size(), core::id::to_string(), core::scoring::Energies::total_energies(), TR(), core::scoring::Energies::weights(), core::scoring::ScoreFunction::weights(), and core::conformation::Residue::xyz().

Referenced by off_rotamer_pack_optimize().

create_minimization_graph()

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
	)

References core::pack::task::PackerTask::being_packed(), core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::residue(), core::pose::Pose::residue_data(), core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), core::scoring::ScoreFunction::setup_for_minimizing_for_node(), core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge(), and core::pose::Pose::size().

Referenced by min_pack_setup().

create_packer_graph() [1/2]

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::minimization_packing::BoltzmannRotamerMover::apply(), protocols::RotamerDump::RotamerDumpMover::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(), core::pack::guidance_scoreterms::sap::SapConstraintHelper::fill_atom_neighbor_stuff(), 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(), core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data(), rotamer_trials(), core::pack::RTMin::rtmin(), protocols::hbnet::HBNet::run(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::rotamer_recovery::RRProtocolRTMin::run(), protocols::simple_moves::ExplicitWaterMover::setup_pack(), and symmetric_rotamer_trials().

create_packer_graph() [2/2]

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
	)

Constructs a graph where edges represent the possibility of interactions between residue pairs.

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), protocols::mean_field::max(), core::scoring::ScoreFunction::max_atomic_interaction_cutoff(), core::conformation::residue_point_graph_from_conformation(), and core::conformation::Conformation::structure_moved().

create_scmin_minimizer_map()

scmin::SCMinMinimizerMapOP core::pack::create_scmin_minimizer_map	(	pose::Pose const &	pose,
		task::PackerTaskCOP	task,
		bool	cartesian
	)

References core::conformation::Residue::natoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by min_pack_setup().

figure_out_repackable_residues()

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::chemical::ResidueType::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::first_sidechain_atom(), core::id::AtomID_Map< T >::get(), core::chemical::ResidueType::is_virtual(), core::chemical::AtomType::name(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and TR().

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

find_residue_max_radii()

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(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexpack_neighbor_graph(), and core::pack::guidance_scoreterms::lk_dome::LK_DomeHelper::prepare_score_data().

get_residue_current_energy()

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
	)

References core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::ResidueAtomTreeCollection::active_residue(), core::pack::scmin::ResidueAtomTreeCollection::active_residue_data(), core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::pack::scmin::SCMinMinimizerMap::clear_active_dofs(), compare_mingraph_and_energy_graph(), core::pack::scmin::ResidueAtomTreeCollectionMomento::coord(), core::kinematics::tree::distance_squared(), core::pack::scmin::SCMinMinimizerMap::make_multifunc(), core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), core::conformation::Residue::natoms(), core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(), reinitialize_mingraph_neighborhood_for_residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(), core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::SCMinMinimizerMap::setup(), core::pack::scmin::SCMinMinimizerMap::starting_dofs(), core::pack::scmin::ResidueAtomTreeCollection::update_from_momento(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by minimize_alt_rotamer().

get_rotamer_angle_diffs()

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

Get rotamer angle differences.

Outer vector is pose length, inner vector is different chi's

References core::conformation::Residue::chi(), core::conformation::Residue::name3(), core::pose::nres_protein(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), and TR().

Referenced by residue_rotamer_recovery(), and rotamer_recovery().

get_total_energy_for_state()

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
	)

References core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::ResidueAtomTreeCollection::active_residue(), core::pack::scmin::ResidueAtomTreeCollection::active_residue_data(), core::pack::scmin::SCMinMinimizerMap::clear_active_dofs(), core::pack::scmin::SCMinMinimizerMap::make_multifunc(), core::pack::rotamer_set::RotamerSets::moltenres_2_resid(), core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), core::pack::rotamer_set::RotamerSets::nmoltenres(), core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(), reinitialize_mingraph_neighborhood_for_residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(), core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::SCMinMinimizerMap::setup(), core::pack::scmin::SCMinMinimizerMap::starting_dofs(), and core::pack::scmin::ResidueAtomTreeCollection::update_from_momento().

Referenced by assign_random_rotamers(), and min_pack_optimize().

initialize_temperatures()

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

(

)

Referenced by min_pack_optimize().

initialize_temperatures_off_rotamer_pack()

utility::vector1< Real > core::pack::initialize_temperatures_off_rotamer_pack

(

)

Referenced by off_rotamer_pack_optimize().

make_new_symmetric_PackerTask_by_intersection()

task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_intersection	(	pose::Pose const &	pose,
		task::PackerTaskCOP	non_symmetric_task
	)

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), and core::pose::Pose::size().

Referenced by make_new_symmetric_PackerTask_by_requested_method().

make_new_symmetric_PackerTask_by_requested_method()

task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_requested_method	(	pose::Pose const &	pose,
		task::PackerTaskCOP	non_symmetric_task
	)

References core::pose::symmetry::is_symmetric(), make_new_symmetric_PackerTask_by_intersection(), and make_new_symmetric_PackerTask_by_union().

Referenced by protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::calc_taskop_movers::ConsensusDesignMover::create_consensus_design_task(), protocols::nmr::filter_spinlabel_ensemble_by_packerenergy(), make_symmetric_task(), pack_rotamers(), protocols::loop_grower::LoopGrower::refine_cycle(), and symmetric_rotamer_trials().

make_new_symmetric_PackerTask_by_truncation()

task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_truncation	(	pose::Pose const &	pose,
		task::PackerTaskCOP	non_symmetric_task
	)

References core::pose::symmetry::is_symmetric(), and make_symmetric_PackerTask_by_truncation().

make_new_symmetric_PackerTask_by_union()

task::PackerTaskOP core::pack::make_new_symmetric_PackerTask_by_union	(	pose::Pose const &	pose,
		task::PackerTaskCOP	non_symmetric_task
	)

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), and core::pose::Pose::size().

Referenced by make_new_symmetric_PackerTask_by_requested_method().

make_symmetric_PackerTask_by_truncation()

void core::pack::make_symmetric_PackerTask_by_truncation	(	pose::Pose const &	pose,
		pack::task::PackerTaskOP	task
	)

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), and core::pose::Pose::size().

Referenced by protocols::task_operations::StoreCombinedStoredTasksMover::apply(), protocols::task_operations::StoreCompoundTaskMover::apply(), protocols::task_operations::StoreTaskMover::apply(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), protocols::pose_metric_calculators::RotamerBoltzCalculator::create_rotamer_set(), protocols::pose_metric_calculators::RotamerBoltzCalculator::init_task(), make_new_symmetric_PackerTask_by_truncation(), protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(), protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap(), and protocols::simple_ddg::ddG::setup_task().

make_symmetric_task()

task::PackerTaskOP core::pack::make_symmetric_task	(	pose::Pose const &	pose,
		task::PackerTaskCOP	task
	)

Make a task symmetric (Using the logic of PackRotamersMover)

This is robust to being passed a non-symmetric pose

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), make_new_symmetric_PackerTask_by_requested_method(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), and protocols::minimization_packing::PackRotamersMover::setup().

min_pack()

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().

Referenced by protocols::coupled_moves::CoupledMovesProtocol::apply(), protocols::minimization_packing::MinPackMover::apply(), and protocols::rotamer_recovery::RRProtocolMinPack::run().

min_pack_optimize()

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
	)

References core::pack::scmin::SidechainStateAssignment::any_unassigned(), core::pack::scmin::SidechainStateAssignment::assign_energy(), assign_random_rotamers(), core::pack::scmin::SidechainStateAssignment::assign_state(), compare_mingraph_and_energy_graph(), core::kinematics::tree::distance_squared(), core::pose::Pose::energies(), core::pack::scmin::SidechainStateAssignment::energy(), get_total_energy_for_state(), initialize_temperatures(), minimize_alt_rotamer(), core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), n_inner_iterations(), core::scoring::n_score_types, core::pack::scmin::SidechainStateAssignment::n_unassigned(), core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(), pass_metropolis(), reinitialize_mingraph_neighborhood_for_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::rg, setup_bgres_cops(), core::scoring::EMapVector::show_weighted(), core::pose::Pose::size(), core::pack::scmin::SidechainStateAssignment::state_momento(), core::scoring::Energies::total_energies(), core::scoring::ScoreFunction::weights(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by min_pack().

min_pack_place_opt_rotamers_on_pose()

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
	)

References core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), core::pose::Pose::replace_residue(), and TR().

Referenced by min_pack().

min_pack_setup()

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
	)

References create_minimization_graph(), create_packer_graph(), create_scmin_minimizer_map(), pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::ready_for_nonideal_scoring(), core::scoring::ScoreFunction::setup_for_packing(), and core::pose::Pose::update_residue_neighbors().

Referenced by min_pack().

minimize_alt_rotamer()

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
	)

References core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs(), core::pack::scmin::ResidueAtomTreeCollection::active_residue(), core::pack::scmin::ResidueAtomTreeCollection::active_residue_data(), core::pack::scmin::SidechainStateAssignment::any_unassigned(), core::pack::scmin::SCMinMinimizerMap::clear_active_dofs(), get_residue_current_energy(), core::pack::scmin::SCMinMinimizerMap::make_multifunc(), reinitialize_mingraph_neighborhood_for_residue(), core::pack::rotamer_set::RotamerSets::rotamer_for_moltenres(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::optimization::Minimizer::run(), core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(), core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue(), core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(), core::pack::scmin::SCMinMinimizerMap::setup(), core::pack::scmin::SCMinMinimizerMap::starting_dofs(), and core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree().

Referenced by assign_random_rotamers(), and min_pack_optimize().

n_inner_iterations()

Size core::pack::n_inner_iterations	(	Real	,
		Size	nrotamers
	)

Referenced by min_pack_optimize(), and off_rotamer_pack_optimize().

off_rotamer_pack()

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().

off_rotamer_pack_optimize()

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
	)

References core::pack::scmin::SidechainStateAssignment::any_unassigned(), core::pack::scmin::SidechainStateAssignment::assign_energy(), assign_random_continuous_rotamer(), core::pack::scmin::SidechainStateAssignment::assign_state(), core::pack::interaction_graph::SimpleInteractionGraph::commit_change(), compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(), core::pack::scmin::SidechainStateAssignment::energy(), initialize_temperatures_off_rotamer_pack(), core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), n_inner_iterations(), core::pack::scmin::SidechainStateAssignment::n_unassigned(), core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(), pass_metropolis(), core::pack::interaction_graph::SimpleInteractionGraph::reject_change(), core::pose::Pose::replace_residue(), core::scoring::rg, core::pack::scmin::SidechainStateAssignment::state_momento(), and core::pack::interaction_graph::SimpleInteractionGraph::total_energy().

Referenced by off_rotamer_pack().

off_rotamer_pack_setup()

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
	)

References create_packer_graph(), core::scoring::npd_hbond, core::scoring::npd_hbond_bb_sc, core::scoring::npd_hbond_lr_bb, core::scoring::npd_hbond_sc, core::scoring::npd_hbond_sr_bb, pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::setup_for_packing(), and core::scoring::ScoreFunction::weights().

Referenced by off_rotamer_pack().

off_rotamer_pack_update_pose()

void core::pack::off_rotamer_pack_update_pose	(	pose::Pose &	pose,
		rotamer_set::ContinuousRotamerSets const &	rotsets,
		scmin::AtomTreeCollectionOP	atc,
		scmin::SidechainStateAssignment const &	best_state
	)

References core::pack::rotamer_set::ContinuousRotamerSets::moltenresid_2_resid(), core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(), core::pack::rotamer_set::ContinuousRotamerSets::nmoltenres(), and core::pose::Pose::replace_residue().

Referenced by off_rotamer_pack().

optimize_H_and_notify()

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

Call optimizeH and tell the user what chi angles have changed.

References core::conformation::Residue::chi(), core::conformation::Residue::chi_atoms(), core::scoring::ScoreFunctionFactory::create_score_function(), core::chemical::element::F, core::scoring::get_score_function(), core::chemical::element::I, core::chemical::ResidueType::is_proton_chi(), core::chemical::ResidueType::n_proton_chi(), core::conformation::Residue::name(), core::conformation::Residue::nchi(), optimizeH(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::conformation::Residue::type().

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

optimizeH()

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().

pack_missing_sidechains()

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().

pack_rotamers()

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::abinitio::DomainAssembly::apply(), protocols::comparative_modeling::LoopRelaxThreadingMover::apply(), protocols::docking::membrane::MPFindInterfaceMover::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_Backrub::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::membrane::MPQuickRelaxMover::apply(), protocols::membrane::MPMutateRelaxMover::apply(), protocols::seeded_abinitio::SeedSetupMover::apply(), protocols::simple_moves::ProlineFixMover::apply(), protocols::simple_filters::SAXSScoreFilter::apply(), protocols::loops::loop_mover::refine::RepackTrial::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), protocols::minimization_packing::RepackSidechainsMover::apply(), protocols::protein_interface_design::movers::BuildAlaPose::apply(), protocols::protein_interface_design::movers::DesignMinimizeHbonds::apply(), protocols::protein_interface_design::movers::RepackMinimize::apply(), protocols::unfolded_state_energy_calculator::UnfoldedStateEnergyCalculatorMover::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::DdGScan::ddG_for_single_residue(), protocols::simple_ddg::AlaScan::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_optH(), 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().

pack_rotamers_cleanup()

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

pack_rotamers_loop() [1/3]

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().

pack_rotamers_loop() [2/3]

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().

pack_rotamers_loop() [3/3]

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().

pack_rotamers_run() [1/2]

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,
		annealer::AnnealerObserverOP	observer
	)

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::size().

Referenced by protocols::RotamerDump::RotamerDumpMover::get_annealer_pick_table(), protocols::pack_daemon::BasicSimAnnealerRepacker::repack(), protocols::pack_daemon::DenseIGRepacker::repack(), protocols::pack_daemon::DoubleDenseIGRepacker::repack(), protocols::minimization_packing::PackRotamersMover::run(), protocols::multistate_design::PackingState::run_packer(), and protocols::minimization_packing::GreenPacker::run_sa().

pack_rotamers_run() [2/2]

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,
		annealer::AnnealerObserverOP	observer,
		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().

pack_rotamers_setup() [1/2]

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().

pack_rotamers_setup() [2/2]

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
	)

Get rotamers, compute energies.

Note

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

References create_packer_graph(), protocols::abinitio::filename(), pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::setup_for_packing(), core::scoring::ScoreFunction::setup_for_packing_with_rotsets(), tt(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::mean_field::MeanField::build_rot_matrix_for_pose(), protocols::quantum_annealing::InteractionGraphSummaryMetric::calculate(), protocols::multistate_design::PackingState::create_packer_data(), protocols::pack_daemon::PackDaemon::setup(), protocols::minimization_packing::PackRotamersMover::setup(), and protocols::minimization_packing::RotamerizeMover::setup().

pack_scorefxn_pose_handshake()

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 protocols::RotamerDump::RotamerDumpMover::apply(), protocols::minimization_packing::GreenPacker::create_fresh_task(), protocols::minimization_packing::GreenPacker::create_reference_packer_task(), min_pack_setup(), off_rotamer_pack_setup(), pack_rotamers(), pack_rotamers_setup(), rotamer_trials(), protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability(), and symmetric_rotamer_trials().

pass_metropolis()

bool core::pack::pass_metropolis	(	Real	temperature,
		Real	deltaE
	)

References protocols::simple_moves::bb_sampler::probability, and core::scoring::rg.

Referenced by min_pack_optimize(), off_rotamer_pack_optimize(), core::pack::annealer::SimAnnealerBase::pass_metropolis(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::FixbbPwatSimAnnealer::run(), core::pack::annealer::FixbbSimAnnealer::run(), core::pack::annealer::SequenceSymmetricAnnealer::run(), core::pack::annealer::SmartFixbbSimAnnealer::run(), and core::pack::annealer::MultiCoolAnnealer::run_constant_temp_rotamer_substitutions().

reinitialize_mingraph_neighborhood_for_residue()

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
	)

References core::scoring::MinimizationGraph::get_minimization_node(), core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), and core::conformation::Residue::seqpos().

Referenced by get_residue_current_energy(), get_total_energy_for_state(), min_pack_optimize(), minimize_alt_rotamer(), and core::pack::RTMin::rtmin().

repackable_residues()

utility::vector1< uint > core::pack::repackable_residues

(

task::PackerTask const &

the_task

)

References core::pack::task::PackerTask::num_to_be_packed(), core::pack::task::PackerTask::pack_residue(), and core::pack::task::PackerTask::total_residue().

Referenced by rotamer_trials().

repackable_residues_dup()

utility::vector1< uint > core::pack::repackable_residues_dup

(

task::PackerTask const &

the_task

)

References core::pack::task::PackerTask::num_to_be_packed(), core::pack::task::PackerTask::pack_residue(), and core::pack::task::PackerTask::total_residue().

Referenced by core::pack::RTMin::rtmin().

residue_rotamer_recovery()

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().

rotamer_recovery()

core::Real core::pack::rotamer_recovery	(	Pose &	pose,
		Pose &	ref_pose,
		core::Real	difference
	)

Percentage of rotamers recovered.

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

Referenced by protocols::rotamer_recovery::RotamerRecovery::init_rotamer_recovery_with_options(), and protocols::features::RotamerRecoveryFeatures::report_features().

rotamer_trials()

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::LoopMover_Refine_KIC::apply(), protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::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().

setup_bgres_cops()

utility::vector1< conformation::ResidueCOP > core::pack::setup_bgres_cops	(	pose::Pose const &	pose,
		task::PackerTask const &	task
	)

References core::pack::task::PackerTask::being_packed(), core::conformation::Residue::clone(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by min_pack_optimize().

symmetric_repackable_residues()

utility::vector1< uint > core::pack::symmetric_repackable_residues	(	task::PackerTask const &	the_task,
		pose::Pose &	pose
	)

References core::pose::Pose::conformation(), core::pack::task::PackerTask::pack_residue(), and core::pack::task::PackerTask::total_residue().

Referenced by symmetric_rotamer_trials().

symmetric_rotamer_trials()

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

References protocols::mean_field::arg_min(), core::pose::Pose::conformation(), create_packer_graph(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), make_new_symmetric_PackerTask_by_requested_method(), pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), protocols::rigid::random, core::pose::Pose::replace_residue(), core::scoring::rg, core::scoring::ScoreFunction::setup_for_packing(), symmetric_repackable_residues(), core::scoring::ScoreFunction::update_residue_for_packing(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::minimization_packing::RotamerTrialsMover::apply(), protocols::minimization_packing::EnergyCutRotamerTrialsMover::apply(), and rotamer_trials().

TR() [1/5]

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

TR() [2/5]

static basic::Tracer core::pack::TR ( "core.pack.min_pack"  , basic::t_info    )

static

Referenced by compare_mingraph_and_energy_graph(), compare_simple_inteaction_graph_alt_state_and_energy_graph(), figure_out_repackable_residues(), get_rotamer_angle_diffs(), min_pack_place_opt_rotamers_on_pose(), off_rotamer_pack(), optimize_H_and_notify(), core::pack::annealer::SmartFixbbSimAnnealer::perform_validation_test(), residue_rotamer_recovery(), rotamer_recovery(), rotamer_trials(), core::pack::annealer::FixbbCoupledRotamerSimAnnealer::run(), core::pack::annealer::FixbbLinkingRotamerSimAnnealer::run(), core::pack::annealer::SmartFixbbSimAnnealer::run(), and core::pack::annealer::FixbbLinkingRotamerSimAnnealer::setup_rotamer_links().

TR() [3/5]

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

static

TR() [4/5]

static basic::Tracer core::pack::TR ( "core.pack.rtmin"  )

static

TR() [5/5]

static basic::Tracer core::pack::TR ( "core.pack.util"  )

static

tt()

static basic::Tracer core::pack::tt ( "core.pack.pack_rotamers"  , basic::t_info    )

static

Referenced by protocols::simple_moves::TailsScoreMover::apply(), protocols::hybridization::TMalign::Kabsch(), pack_rotamers_loop(), pack_rotamers_setup(), and protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score().