Namespaces
	annealer

	dunbrack

	interaction_graph

	rotamer_set

	scmin

	task

Classes
class	RTMin

Typedefs
typedef conformation::symmetry::SymmetricConformation	SymmetricConformation

typedef conformation::symmetry::SymmetryInfo	SymmetryInfo

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

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

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

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

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

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

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

static numeric::random::RandomGenerator	RG (22307)

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

scoring::MinimizationGraphOP	create_minimization_graph (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTask const &task, graph::Graph const &packer_neighbor_graph, scmin::SCMinMinimizerMap const &sc_min_map)

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

utility::vector1< Real >	initialize_temperatures ()

utility::vector1< Real >	initialize_temperatures_stochastic_pack ()

Real	get_residue_current_energy (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets, Size resid, Size moltenres_id)

Real	get_total_energy_for_state (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets)

Real	minimize_alt_rotamer (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > const &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraph &mingraph, scmin::SCMinMinimizerMap &scminmap, optimization::MinimizerOptions const &min_options, scmin::SidechainStateAssignment const &curr_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSets const &rotsets, Size resid, Size moltenres_id, Size rotamer_state_on_moltenres)

bool	pass_metropolis (Real temperature, Real deltaE)

Size	n_inner_iterations (Real, Size nrotamers)

void	assign_random_rotamers (pose::Pose &pose, utility::vector1< conformation::ResidueCOP > &bgres, scoring::ScoreFunction const &sfxn, scoring::MinimizationGraphOP mingraph, scmin::SCMinMinimizerMapOP scminmap, optimization::MinimizerOptions const &min_options, scmin::SidechainStateAssignment &curr_state, scmin::SidechainStateAssignment &best_state, scmin::AtomTreeCollectionOP atc, rotamer_set::RotamerSetsCOP rotsets)

void	min_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task, bool cartesian=false, bool nonideal=false)
	Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm. More...

void	compare_simple_inteaction_graph_alt_state_and_energy_graph (Size resid, pose::Pose const &pose, scoring::ScoreFunction const &sfxn, interaction_graph::SimpleInteractionGraph const &ig)

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

void	stochastic_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task)

static basic::Tracer	TR ("core.io.pdb.file_data")

void	optimize_H_and_notify (pose::Pose &pose, id::AtomID_Mask const &missing)
	Call optimizeH and tell the user what chi angles have changed. More...

void	optimizeH (pose::Pose &pose, scoring::ScoreFunction const &sfxn)
	This function will optimize the placement of all movable hydrogen atoms. This includes the hydroxyl hydrogens as well as the HIS protonation state. If the -flip_HNQ flag is on the command line, then it will also consider the flip states of histadine, asparagine and glutamine, (nearly) as described by Word et al. 1999. More...

void	pack_missing_sidechains (pose::Pose &pose, id::AtomID_Mask const &missing)
	This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask) More...

bool	figure_out_repackable_residues (core::pose::Pose &pose, core::id::AtomID_Mask const &to_repack, utility::vector1_bool &repackable)
	return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb More...

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

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

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

void	pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results)

void	pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > &pose_list)

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

void	setup_IG_res_res_weights (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::RotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig)
	upweights certain edges in the interaction graph if this is specified in the task More...

Real	pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack=utility::vector0< int >())
	Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose. More...

void	pack_rotamers_run (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy)
	Runs simulated annealing and returns the. More...

void	symmetric_pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP non_symmetric_task)

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

Real	symmetric_pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack)

graph::GraphOP	create_packer_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task)
	Constructs a graph where edges represent the possibility of interactions between residue pairs. More...

graph::GraphOP	create_packer_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, core::Size total_nodes, utility::vector1< Distance > const &residue_radii)
	Constructs a graph where edges represent the possibility of interactions between residue pairs. More...

utility::vector1< 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 numeric::random::RandomGenerator	rottrials_RG (10801)

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 numeric::random::RandomGenerator	rtmin_RG (206025)

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, scoring::MinimizationGraph &mingraph)

Typedef Documentation

typedef conformation::symmetry::SymmetricConformation core::pack::SymmetricConformation

Definition at line 69 of file rotamer_trials.cc.

typedef conformation::symmetry::SymmetryInfo core::pack::SymmetryInfo

Definition at line 70 of file rotamer_trials.cc.

Function Documentation

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

Definition at line 1046 of file min_pack.cc.

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(), 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 stochastic_pack().

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
	)

Definition at line 689 of file min_pack.cc.

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(), RG(), core::pack::scmin::SidechainStateAssignment::state_momento(), and core::scoring::ScoreFunction::weights().

Referenced by min_pack().

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

Definition at line 606 of file min_pack.cc.

References core::graph::Node::const_edge_list_end(), 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::EnergyEdge::fill_energy_map(), core::graph::Graph::find_edge(), core::scoring::MinimizationGraph::get_minimization_node(), core::graph::Edge::get_node(), core::scoring::hbond_bb_sc, core::scoring::Energies::onebody_energies(), core::pose::Pose::residue(), core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::total_score, core::scoring::ScoreFunction::weights(), and core::scoring::Energies::weights().

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

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
	)

Definition at line 977 of file min_pack.cc.

References core::graph::Node::const_edge_list_end(), core::scoring::EMapVector::dot(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::EnergyEdge::fill_energy_map(), core::graph::Graph::find_edge(), core::graph::Edge::get_node(), core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node(), core::scoring::Energies::onebody_energies(), core::pack::interaction_graph::SimpleNode::proposed_one_body_energy(), core::scoring::EMapVector::show_if_nonzero_weight(), core::scoring::ScoreFunction::weights(), and core::scoring::Energies::weights().

Referenced by stochastic_pack().

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
	)

Definition at line 114 of file min_pack.cc.

References core::pack::task::PackerTask::being_packed(), core::graph::Graph::const_edge_list_begin(), core::graph::Graph::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::pose::Pose::residue(), 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::total_residue().

Referenced by min_pack().

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.

Definition at line 52 of file packer_neighbors.cc.

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

Referenced by protocols::RotamerDump::RotamerDumpMover::apply(), protocols::simple_filters::PackerNeighborGraphFilter::apply(), core::pack::rotamer_set::bb_independent_rotamers(), protocols::motifs::Motif::build_rotamers(), protocols::motifs::build_rotamers_lite(), protocols::jumping::ResiduePairJump::build_sidechain_rotamers(), protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(), protocols::simple_moves::GreenPacker::create_fresh_packer_neighbor_graph(), protocols::simple_moves::GreenPacker::create_reference_packer_neighbor_graph(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexpack_neighbor_graph(), protocols::optimize_weights::IterativeOptEDriver::get_nat_aa_opte_data(), protocols::optimize_weights::IterativeOptEDriver::get_nat_rot_opte_data(), min_pack(), pack_rotamers_setup(), rotamer_trials(), core::pack::RTMin::rtmin(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::rotamer_recovery::RRProtocolRTMin::run(), stochastic_pack(), symmetric_pack_rotamers_setup(), and symmetric_rotamer_trials().

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.

Definition at line 66 of file packer_neighbors.cc.

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::ScoreFunction::info(), core::conformation::residue_point_graph_from_conformation(), core::conformation::Conformation::structure_moved(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

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

Definition at line 84 of file min_pack.cc.

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

Referenced by min_pack().

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

Definition at line 74 of file pack_missing_sidechains.cc.

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.

Definition at line 142 of file packer_neighbors.cc.

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
	)

Definition at line 301 of file min_pack.cc.

Referenced by minimize_alt_rotamer().

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
	)

Definition at line 430 of file min_pack.cc.

Referenced by assign_random_rotamers(), and min_pack().

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

Definition at line 226 of file min_pack.cc.

Referenced by min_pack().

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

Definition at line 254 of file min_pack.cc.

Referenced by stochastic_pack().

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

Definition at line 113 of file make_symmetric_task.cc.

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pack::task::PackerTask_::nonconst_residue_task(), core::pack::task::ResidueLevelTask::prevent_repacking(), core::pack::task::PackerTask_::residue_task(), core::pack::task::PackerTask_::symmetrize_by_intersection(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), core::pack::task::PackerTask_::update_commutative(), and core::pack::task::PackerTask_::update_residue_intersection().

Referenced by 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
	)

Definition at line 148 of file make_symmetric_task.cc.

References core::pose::symmetry::is_symmetric(), make_new_symmetric_PackerTask_by_intersection(), make_new_symmetric_PackerTask_by_union(), core::pack::task::PackerTask_::symmetrize_by_intersection(), and core::pack::task::PackerTask_::symmetrize_by_union().

Referenced by protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::simple_moves::ConsensusDesignMover::create_consensus_design_task(), symmetric_pack_rotamers(), and symmetric_rotamer_trials().

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

Definition at line 66 of file make_symmetric_task.cc.

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

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

Definition at line 78 of file make_symmetric_task.cc.

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pack::task::PackerTask_::nonconst_residue_task(), core::pack::task::ResidueLevelTask::prevent_repacking(), core::pack::task::PackerTask_::residue_task(), core::pack::task::PackerTask_::symmetrize_by_union(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), core::pack::task::PackerTask_::update_commutative(), and core::pack::task::PackerTask_::update_residue_union().

Referenced by make_new_symmetric_PackerTask_by_requested_method().

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

Definition at line 44 of file make_symmetric_task.cc.

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight(), make_new_symmetric_PackerTask_by_truncation(), and protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap().

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.

Definition at line 750 of file min_pack.cc.

References assign_random_rotamers(), compare_mingraph_and_energy_graph(), create_minimization_graph(), create_packer_graph(), create_scmin_minimizer_map(), core::kinematics::tree::distance_squared(), core::pose::Pose::energies(), get_total_energy_for_state(), initialize_temperatures(), core::optimization::MinimizerOptions::max_iter(), minimize_alt_rotamer(), n_inner_iterations(), core::scoring::n_score_types, pack_scorefxn_pose_handshake(), pass_metropolis(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), RG(), setup_bgres_cops(), core::scoring::ScoreFunction::setup_for_packing(), core::scoring::EMapVector::show_weighted(), core::optimization::MinimizerOptions::silent(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), TR(), core::pose::Pose::update_residue_neighbors(), core::scoring::ScoreFunction::weights(), protocols::kinmatch::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::simple_moves::MinPackMover::apply(), and protocols::rotamer_recovery::RRProtocolMinPack::run().

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
	)

Definition at line 487 of file min_pack.cc.

Referenced by assign_random_rotamers(), and min_pack().

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

Definition at line 590 of file min_pack.cc.

Referenced by min_pack(), and stochastic_pack().

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.

Definition at line 56 of file optimizeH.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), optimizeH(), core::pose::Pose::residue(), core::scoring::SCORE12_PATCH, core::scoring::STANDARD_WTS, core::pose::Pose::total_residue(), and TR().

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

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.

Definition at line 105 of file optimizeH.cc.

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

Definition at line 50 of file pack_missing_sidechains.cc.

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

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

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

Definition at line 74 of file pack_rotamers.cc.

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

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

Definition at line 109 of file pack_rotamers.cc.

Referenced by protocols::ddg::ddGMover::apply(), protocols::swa::protein::StepWiseProteinResidueSampler::initialize_for_regular_packer(), pack_rotamers_loop(), protocols::ddg::ddGMover::relax_wildtype_structure(), and protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability().

void core::pack::pack_rotamers_loop	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	scfxn,
		task::PackerTaskCOP	task,
		Size const	nloop,
		utility::vector1< std::pair< Real, std::string > > &	results
	)

Definition at line 123 of file pack_rotamers.cc.

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
	)

Definition at line 138 of file pack_rotamers.cc.

References core::conformation::Residue::name1(), pack_rotamers_run(), pack_rotamers_setup(), core::pose::Pose::residue(), run, core::pose::Pose::sequence(), setup_IG_res_res_weights(), core::pose::Pose::total_residue(), and tt().

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.

Definition at line 273 of file pack_rotamers.cc.

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

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

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.

Definition at line 309 of file pack_rotamers.cc.

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
	)

Definition at line 189 of file pack_rotamers.cc.

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

Referenced by protocols::multistate_design::PackingState::create_packer_data(), pack_rotamers(), pack_rotamers_loop(), protocols::pack_daemon::PackDaemon::setup(), and protocols::simple_moves::PackRotamersMover::setup().

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.

Definition at line 219 of file packer_neighbors.cc.

Referenced by protocols::RotamerDump::RotamerDumpMover::apply(), protocols::simple_moves::GreenPacker::create_fresh_task(), protocols::simple_moves::GreenPacker::create_reference_packer_task(), min_pack(), pack_rotamers(), pack_rotamers_setup(), rotamer_trials(), protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability(), stochastic_pack(), symmetric_pack_rotamers(), symmetric_pack_rotamers_setup(), and symmetric_rotamer_trials().

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

Definition at line 568 of file min_pack.cc.

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
	)

Definition at line 674 of file rtmin.cc.

References core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), core::scoring::MinimizationGraph::get_minimization_node(), core::graph::Graph::get_node(), core::scoring::MinimizationEdge::reinitialize_active_energy_methods(), core::scoring::ScoreFunction::reinitialize_minnode_for_residue(), core::conformation::Residue::seqpos(), and core::scoring::MinimizationEdge::setup_for_minimizing().

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

utility::vector1< uint > core::pack::repackable_residues ( task::PackerTask const & the_task)

Definition at line 184 of file rotamer_trials.cc.

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().

utility::vector1< uint > core::pack::repackable_residues_dup ( task::PackerTask const & the_task)

Definition at line 711 of file rtmin.cc.

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().

static numeric::random::RandomGenerator core::pack::RG ( 22307 )

static

Referenced by assign_random_continuous_rotamer(), assign_random_rotamers(), core::pack::dunbrack::SingleResidueDunbrackLibrary::hokey_template_workaround(), min_pack(), pass_metropolis(), and stochastic_pack().

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

Definition at line 83 of file rotamer_trials.cc.

References create_packer_graph(), 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::pose::Pose::residue(), rottrials_RG(), core::scoring::ScoreFunction::setup_for_packing(), symmetric_rotamer_trials(), TR(), core::scoring::ScoreFunction::update_residue_for_packing(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::loops::loop_mover::refine::SmallMinCCDTrial::apply(), protocols::loops::loop_mover::refine::ShearMinCCDTrial::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::RotamerTrialsMover::apply(), protocols::simple_moves::EnergyCutRotamerTrialsMover::apply(), protocols::swa::protein::StepWiseProteinPacker::apply_regular_packer(), protocols::swa::protein::StepWiseProteinResidueSampler::apply_regular_packer(), protocols::swa::rna::o2star_minimize(), protocols::rna::RNA_Minimizer::o2star_trials(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::restrict_sequence_profile(), protocols::rotamer_recovery::RRProtocolRotamerTrials::run(), protocols::swa::rna::StepWiseRNA_AnalyticalLoopCloseSampler::sample_o2star_hydrogen(), and protocols::swa::rna::StepWiseRNA_ResidueSampler::sample_o2star_hydrogen().

static numeric::random::RandomGenerator core::pack::rottrials_RG ( 10801 )

static

Referenced by rotamer_trials(), and symmetric_rotamer_trials().

static numeric::random::RandomGenerator core::pack::rtmin_RG ( 206025 )

static

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

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

Definition at line 212 of file min_pack.cc.

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

Referenced by min_pack().

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

Definition at line 240 of file pack_rotamers.cc.

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

Referenced by pack_rotamers_loop(), protocols::simple_moves::symmetry::SymPackRotamersMover::setup(), and protocols::simple_moves::PackRotamersMover::setup().

void core::pack::stochastic_pack	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	sfxn,
		task::PackerTaskCOP	task
	)

Definition at line 1094 of file min_pack.cc.

References assign_random_continuous_rotamer(), core::pack::interaction_graph::SimpleInteractionGraph::commit_change(), compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(), core::graph::Graph::copy_connectivity(), create_packer_graph(), core::pack::rotamer_set::ContinuousRotamerSets::full_sample_rot_index_2_moltenres_sample_rot_index(), initialize_temperatures_stochastic_pack(), core::pack::rotamer_set::ContinuousRotamerSets::moltenres_for_sample_rot(), core::pack::rotamer_set::ContinuousRotamerSets::moltenresid_2_resid(), n_inner_iterations(), core::pack::rotamer_set::ContinuousRotamerSets::n_sample_rotamers(), core::pack::rotamer_set::ContinuousRotamerSets::nmoltenres(), pack_scorefxn_pose_handshake(), pass_metropolis(), core::pack::interaction_graph::SimpleInteractionGraph::reject_change(), core::pose::Pose::replace_residue(), RG(), core::pack::rotamer_set::ContinuousRotamerSets::rotamer_set_for_moltenres(), core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize(), core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction(), core::scoring::ScoreFunction::setup_for_packing(), core::pack::interaction_graph::SimpleInteractionGraph::total_energy(), and TR().

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

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

Definition at line 350 of file pack_rotamers.cc.

References make_new_symmetric_PackerTask_by_requested_method(), pack_scorefxn_pose_handshake(), symmetric_pack_rotamers_run(), and symmetric_pack_rotamers_setup().

Referenced by protocols::protein_interface_design::movers::RepackMinimize::apply(), pack_rotamers(), and protocols::simple_moves::ddG::symm_ddG().

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
	)

Definition at line 428 of file pack_rotamers.cc.

References core::pose::Pose::conformation(), core::pose::Pose::replace_residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::symmetry::SymPackRotamersMover::run(), and symmetric_pack_rotamers().

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
	)