protocols::toolbox::pose_metric_calculators Namespace Reference

Classes
class	BuriedUnsatisfiedPolarsCalculator
class	CatPiCalculator
class	ChargeCalculator
class	ClashCountCalculator
class	DecomposeAndReweightEnergiesCalculator
class	EmptyVertexData
class	EnergiesData
class	ExplicitWaterUnsatisfiedPolarsCalculator
class	FragQualCalculator
class	HPatchCalculator
class	InterGroupNeighborsCalculator
class	MetricValueGetter
class	NeighborhoodByDistanceCalculator
class	NeighborsByDistanceCalculator
class	NonlocalContactsCalculator
class	NumberHBondsCalculator
class	PackstatCalculator
class	PiPiCalculator
class	ResidueDecompositionByChainCalculator
class	ResidueDecompositionCalculator
class	RotamerBoltzCalculator
class	RotamerRecovery
class	SaltBridgeCalculator
class	SemiExplicitWaterUnsatisfiedPolarsCalculator
class	SequenceComparison
class	SurfaceCalculator

Typedefs
typedef utility::pointer::owning_ptr < DecomposeAndReweightEnergiesCalculator >	DecomposeAndReweightEnergiesCalculatorOP
typedef utility::pointer::owning_ptr < DecomposeAndReweightEnergiesCalculator const >	DecomposeAndReweightEnergiesCalculatorCOP
typedef utility::pointer::owning_ptr < InterGroupNeighborsCalculator >	InterGroupNeighborsCalculatorOP
typedef utility::pointer::owning_ptr < InterGroupNeighborsCalculator const >	InterGroupNeighborsCalculatorCOP
typedef utility::pointer::owning_ptr < NeighborhoodByDistanceCalculator >	NeighborhoodByDistanceCalculatorOP
typedef utility::pointer::owning_ptr < NeighborhoodByDistanceCalculator const >	NeighborhoodByDistanceCalculatorCOP
typedef utility::pointer::owning_ptr < NeighborsByDistanceCalculator >	NeighborsByDistanceCalculatorOP
typedef utility::pointer::owning_ptr < NeighborsByDistanceCalculator const >	NeighborsByDistanceCalculatorCOP
typedef utility::pointer::owning_ptr < ResidueDecompositionByChainCalculator >	ResidueDecompositionByChainCalculatorOP
typedef utility::pointer::owning_ptr < ResidueDecompositionByChainCalculator const >	ResidueDecompositionByChainCalculatorCOP
typedef utility::pointer::owning_ptr < RotamerBoltzCalculator >	RotamerBoltzCalculatorOP
typedef utility::pointer::owning_ptr < RotamerBoltzCalculator const >	RotamerBoltzCalculatorCOP

Functions
void	append_rsd_by_jump_near_atom (pose::Pose &pose, Size seqpos, Size atomno, conformation::Residue new_rsd, Size new_atomno, Real dist_min, Real dist_max)
void	dock_waters_to_atom (pose::Pose &pose, ScoreFunctionOP scorefxn, Size seqpos, Size atomno, conformation::Residue wat_rsd, Size new_atomno, Real dist_min, Real dist_max)
void	find_res_unsat_polars (Pose const pose, Size const seqpos, vector1< bool > &atm_is_unsat)
std::string	choose_hbond_parameter_set ()
	use the "score12_params" set if the -restore_pre_talaris_2013_behavior flag is on the command line and otherwise use the new and improved sp2_elec_params parameter set More...
bool	fast_clash_check (Pose const &pose, vector1< id::AtomID > const check_atids, Real const clash_dist_cut)

Variables
static basic::Tracer	TR ("protocols.toolbox.PoseMetricCalculators.ExplicitWaterUnsatisfiedPolarsCalculator")
static numeric::random::RandomGenerator	RG (2718)
static basic::Tracer	TR ("seqrecovery")

Typedef Documentation

typedef utility::pointer::owning_ptr< DecomposeAndReweightEnergiesCalculator const > protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculatorCOP

typedef utility::pointer::owning_ptr< DecomposeAndReweightEnergiesCalculator > protocols::toolbox::pose_metric_calculators::DecomposeAndReweightEnergiesCalculatorOP

typedef utility::pointer::owning_ptr< InterGroupNeighborsCalculator const > protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculatorCOP

typedef utility::pointer::owning_ptr< InterGroupNeighborsCalculator > protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculatorOP

typedef utility::pointer::owning_ptr< NeighborhoodByDistanceCalculator const > protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculatorCOP

typedef utility::pointer::owning_ptr< NeighborhoodByDistanceCalculator > protocols::toolbox::pose_metric_calculators::NeighborhoodByDistanceCalculatorOP

typedef utility::pointer::owning_ptr< NeighborsByDistanceCalculator const > protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculatorCOP

typedef utility::pointer::owning_ptr< NeighborsByDistanceCalculator > protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculatorOP

typedef utility::pointer::owning_ptr< ResidueDecompositionByChainCalculator const > protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculatorCOP

typedef utility::pointer::owning_ptr< ResidueDecompositionByChainCalculator > protocols::toolbox::pose_metric_calculators::ResidueDecompositionByChainCalculatorOP

typedef utility::pointer::owning_ptr< RotamerBoltzCalculator const > protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculatorCOP

typedef utility::pointer::owning_ptr< RotamerBoltzCalculator> protocols::toolbox::pose_metric_calculators::RotamerBoltzCalculatorOP

Function Documentation

void protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom	(	pose::Pose &	pose,
		Size	seqpos,
		Size	atomno,
		conformation::Residue	new_rsd,
		Size	new_atomno,
		Real	dist_min,
		Real	dist_max
	)

References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_name(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::FoldTree::num_jump(), protocols::geometry::random_reorientation_matrix(), core::pose::Pose::residue(), RG, core::pose::Pose::set_jump(), core::pose::Pose::total_residue(), and numeric::random::RandomGenerator::uniform().

Referenced by dock_waters_to_atom().

std::string protocols::toolbox::pose_metric_calculators::choose_hbond_parameter_set

(

)

use the "score12_params" set if the -restore_pre_talaris_2013_behavior flag is on the command line and otherwise use the new and improved sp2_elec_params parameter set

References basic::options::option, and basic::options::OptionKeys::mistakes::restore_pre_talaris_2013_behavior.

void protocols::toolbox::pose_metric_calculators::dock_waters_to_atom	(	pose::Pose &	pose,
		ScoreFunctionOP	scorefxn,
		Size	seqpos,
		Size	atomno,
		conformation::Residue	wat_rsd,
		Size	new_atomno,
		Real	dist_min,
		Real	dist_max
	)

References append_rsd_by_jump_near_atom(), protocols::simple_moves::MinMover::apply(), protocols::moves::MonteCarlo::boltzmann(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::FoldTree::num_jump(), protocols::moves::MonteCarlo::recover_low(), core::pose::Pose::set_jump(), and core::kinematics::MoveMap::set_jump().

Referenced by protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator::recompute().

bool protocols::toolbox::pose_metric_calculators::fast_clash_check	(	Pose const &	pose,
		vector1< id::AtomID > const	check_atids,
		Real const	clash_dist_cut
	)

References core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_wdepth(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().

void protocols::toolbox::pose_metric_calculators::find_res_unsat_polars	(	Pose const	pose,
		Size const	seqpos,
		vector1< bool > &	atm_is_unsat
	)

References core::pose::Pose::residue(), and core::scoring::hbonds::HBondSet::setup_for_residue_pair_energies().

Referenced by protocols::toolbox::pose_metric_calculators::ExplicitWaterUnsatisfiedPolarsCalculator::recompute().

Variable Documentation

numeric::random::RandomGenerator protocols::toolbox::pose_metric_calculators::RG(2718)

static

Referenced by append_rsd_by_jump_near_atom().

basic::Tracer protocols::toolbox::pose_metric_calculators::TR("protocols.toolbox.PoseMetricCalculators.ExplicitWaterUnsatisfiedPolarsCalculator")

static

Referenced by protocols::toolbox::pose_metric_calculators::BuriedUnsatisfiedPolarsCalculator::assert_calculators(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::assert_calculators(), protocols::toolbox::pose_metric_calculators::SequenceComparison::fill_designable_set(), protocols::toolbox::pose_metric_calculators::SequenceComparison::get_sequence_recovery(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::lookup(), protocols::toolbox::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::toolbox::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::toolbox::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), and protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute().

basic::Tracer protocols::toolbox::pose_metric_calculators::TR("seqrecovery")

static