Namespaces
	annealer

	dunbrack

	interaction_graph

	rotamer_set

	scmin

	task

Classes
class	RTMin

Typedefs
typedef conformation::symmetry::SymmetricConformation	SymmetricConformation

typedef conformation::symmetry::SymmetryInfo	SymmetryInfo

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

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

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

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

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

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

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

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

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

utility::vector1< 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 &pose, scoring::ScoreFunction const &sfxn, interaction_graph::SimpleInteractionGraph const &ig)

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

void	off_rotamer_pack_setup (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task, rotamer_set::ContinuousRotamerSetsOP &rotsets, scmin::AtomTreeCollectionOP &atc, interaction_graph::SimpleInteractionGraphOP &ig)

void	off_rotamer_pack_optimize (rotamer_set::ContinuousRotamerSets const &rotsets, scmin::AtomTreeCollectionOP atc, interaction_graph::SimpleInteractionGraph &ig, scmin::SidechainStateAssignment &best_state)

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

void	off_rotamer_pack (pose::Pose &pose, scoring::ScoreFunction const &sfxn, task::PackerTaskCOP task)
	Interface to a version of the packer that uses very little memory and simultaneously is able to go off rotamer and explore more of sidechain conformation space. Quite a bit faster than the min-packer. More...

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

utility::vector1< 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)

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)

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)

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

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

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

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

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

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

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

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

Typedef Documentation

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

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

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

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(), numeric::random::RandomGenerator::uniform(), and core::pack::scmin::ResidueAtomTreeCollection::update_residue().

Referenced by off_rotamer_pack_optimize().

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(), RG, core::pack::scmin::SidechainStateAssignment::state_momento(), numeric::random::RandomGenerator::uniform(), and core::scoring::ScoreFunction::weights().

Referenced by min_pack_optimize().

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

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

References core::scoring::EMapVector::dot(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Graph::find_edge(), core::pack::interaction_graph::SimpleInteractionGraph::get_simple_node(), core::scoring::Energies::onebody_energies(), core::pack::interaction_graph::SimpleNode::proposed_one_body_energy(), scoring, utility::to_string(), core::scoring::ScoreFunction::weights(), and core::scoring::Energies::weights().

Referenced by off_rotamer_pack_optimize().

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
	)

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(), r1, r2, 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_setup().

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::total_residue().

Referenced by core::pack::rotamer_set::bb_independent_rotamers(), min_pack_setup(), off_rotamer_pack_setup(), pack_rotamers_setup(), rotamer_trials(), core::pack::RTMin::rtmin(), 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.

References core::pose::Pose::conformation(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::scoring::ScoreFunction::info(), utility::max(), max_radius, 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
	)

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

Referenced by min_pack_setup().

bool core::pack::figure_out_repackable_residues	(	core::pose::Pose &	pose,
		core::id::AtomID_Mask const &	to_repack,
		utility::vector1_bool &	repackable
	)

return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb

References core::id::AtomID_Map< T >::get(), core::pose::Pose::residue_type(), restype, core::pose::Pose::total_residue(), and TR.

Referenced by pack_missing_sidechains().

utility::vector1< Distance > core::pack::find_residue_max_radii	(	pose::Pose const &	pose,
		task::PackerTaskCOP	the_task
	)

for each residue in the protein, finds the largest bounding sphere over all allowable rotameric/chemical modifications possible given the input task.

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

Referenced by create_packer_graph().

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

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
	)

Referenced by assign_random_rotamers(), and min_pack_optimize().

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

References minpack_temp_schedule, option, and user.

Referenced by min_pack_optimize().

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

References minpack_temp_schedule, option, and user.

Referenced by off_rotamer_pack_optimize().

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(), core::pack::task::PackerTask_::nonconst_residue_task(), o, 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(), core::pack::task::PackerTask_::update_residue_intersection(), and utility_exit_with_message.

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
	)

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

Referenced by 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
	)

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
	)

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pack::task::PackerTask_::nonconst_residue_task(), o, 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(), core::pack::task::PackerTask_::update_residue_union(), and utility_exit_with_message.

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
	)

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

Referenced by make_new_symmetric_PackerTask_by_truncation().

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

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

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

void core::pack::min_pack_optimize	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		task::PackerTaskOP	task,
		rotamer_set::RotamerSetsOP	rotsets,
		scmin::SCMinMinimizerMapOP	scminmap,
		scoring::MinimizationGraphOP	mingraph,
		scmin::AtomTreeCollectionOP	atc,
		optimization::MinimizerOptions const &	min_options,
		scmin::SidechainStateAssignment &	best_state
	)

void core::pack::min_pack_place_opt_rotamers_on_pose	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		rotamer_set::RotamerSetsOP	rotsets,
		scmin::AtomTreeCollectionOP	atc,
		scmin::SidechainStateAssignment const &	best_state,
		Real	start_score
	)

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

Referenced by min_pack().

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(), minpack_disable_bumpcheck, option, pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::ready_for_nonideal_scoring(), core::scoring::ScoreFunction::setup_for_packing(), core::pose::Pose::update_residue_neighbors(), and utility_exit_with_message.

Referenced by min_pack().

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
	)

Referenced by assign_random_rotamers(), and min_pack_optimize().

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

References minpack_inner_iteration_scale, option, and user.

Referenced by min_pack_optimize(), and off_rotamer_pack_optimize().

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

Interface to a version of the packer that uses very little memory and simultaneously is able to go off rotamer and explore more of sidechain conformation space. Quite a bit faster than the min-packer.

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

void core::pack::off_rotamer_pack_optimize	(	rotamer_set::ContinuousRotamerSets const &	rotsets,
		scmin::AtomTreeCollectionOP	atc,
		interaction_graph::SimpleInteractionGraph &	ig,
		scmin::SidechainStateAssignment &	best_state
	)

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::pack::scmin::SidechainStateAssignment::energy(), core::pack::rotamer_set::ContinuousRotamerSets::full_sample_rot_index_2_moltenres_sample_rot_index(), initialize_temperatures_off_rotamer_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(), 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::total_energy(), and numeric::random::RandomGenerator::uniform().

Referenced by off_rotamer_pack().

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(), pack_scorefxn_pose_handshake(), and core::scoring::ScoreFunction::setup_for_packing().

Referenced by off_rotamer_pack().

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().

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::chemical::element::F, core::scoring::get_score_function(), core::chemical::element::I, score::optH_patch, score::optH_weights, optimizeH(), option, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, core::pose::Pose::residue(), scoring, basic::subtract_degree_angles(), core::pose::Pose::total_residue(), TR, and user.

Referenced by 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.

References option, and pack_rotamers().

Referenced by optimize_H_and_notify().

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

This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask)

this function will run rotamer trials on sidechains with missing density. It first sets up a PackerTask with repacking freedom for residues with sidechain missing atoms in the missing AtomID_Mask, then runs rotamer_trials. This function is smart enough to ignore missing virtual atoms

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

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

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

References core::pose::symmetry::is_symmetric(), basic::PACK_ROTAMERS, pack_rotamers_run(), pack_rotamers_setup(), pack_scorefxn_pose_handshake(), PROF_START, PROF_STOP, and symmetric_pack_rotamers().

Referenced by optimizeH(), pack_missing_sidechains(), and core::util::rebuild_disulfide().

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

References pack_rotamers_loop().

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

References pack_rotamers_loop().

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

References core::chemical::element::F, core::chemical::element::I, 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.

Referenced by pack_rotamers_loop().

Real core::pack::pack_rotamers_run	(	pose::Pose &	pose,
		task::PackerTaskCOP	task,
		rotamer_set::FixbbRotamerSetsCOP	rotsets,
		interaction_graph::InteractionGraphBaseOP	ig,
		utility::vector0< int >	rot_to_pack
	)

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

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

void core::pack::pack_rotamers_run	(	pose::Pose const &	pose,
		task::PackerTaskCOP	task,
		rotamer_set::FixbbRotamerSetsCOP	rotsets,
		interaction_graph::InteractionGraphBaseOP	ig,
		utility::vector0< int >	rot_to_pack,
		ObjexxFCL::FArray1D_int &	bestrotamer_at_seqpos,
		core::PackerEnergy &	bestenergy
	)

Runs simulated annealing and returns the.

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

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

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

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

References create_packer_graph(), basic::options::OptionKeys::packing::dump_rotamer_sets, filename(), basic::GET_ENERGIES, basic::options::option, pack_scorefxn_pose_handshake(), PROF_START, PROF_STOP, core::scoring::ScoreFunction::setup_for_packing(), tt, and core::pose::Pose::update_residue_neighbors().

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

Referenced by pack_rotamers(), and pack_rotamers_loop().

void core::pack::pack_scorefxn_pose_handshake	(	pose::Pose &	pose,
		scoring::ScoreFunction const &	scfxn
	)

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

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

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

References RG, and numeric::random::RandomGenerator::uniform().

Referenced by min_pack_optimize(), and off_rotamer_pack_optimize().

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
	)

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 )

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 )

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().

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

References utility::arg_min(), create_packer_graph(), core::pose::symmetry::is_symmetric(), pack_scorefxn_pose_handshake(), core::scoring::ScoreFunction::prepare_rotamers_for_packing(), PROF_START, PROF_STOP, random_permutation(), repackable_residues(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), basic::ROTAMER_TRIALS, rottrials_RG, core::scoring::ScoreFunction::setup_for_packing(), symmetric_rotamer_trials(), core::scoring::ScoreFunction::update_residue_for_packing(), and core::pose::Pose::update_residue_neighbors().

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::total_residue().

Referenced by min_pack_optimize().

void core::pack::setup_IG_res_res_weights	(	pose::Pose const &	pose,
		task::PackerTaskCOP	task,
		rotamer_set::RotamerSetsCOP	rotsets,
		interaction_graph::InteractionGraphBaseOP	ig
	)

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

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

Referenced by pack_rotamers_loop().

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

References make_new_symmetric_PackerTask_by_requested_method(), basic::PACK_ROTAMERS, pack_scorefxn_pose_handshake(), PROF_START, PROF_STOP, symmetric_pack_rotamers_run(), and symmetric_pack_rotamers_setup().

Referenced by pack_rotamers().

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
	)

References annealer, core::pose::Pose::conformation(), PROF_START, PROF_STOP, core::pose::Pose::replace_residue(), basic::SIMANNEALING, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by 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
	)

References create_packer_graph(), basic::options::OptionKeys::packing::dump_rotamer_sets, filename(), basic::GET_ENERGIES, basic::options::option, pack_scorefxn_pose_handshake(), PROF_START, PROF_STOP, core::scoring::ScoreFunction::setup_for_packing(), tt, and core::pose::Pose::update_residue_neighbors().

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