protocols::toolbox::pose_metric_calculators Namespace Reference

Classes
class	BuriedUnsatisfiedPolarsCalculator
class	CatPiCalculator
class	ChargeCalculator
class	ClashCountCalculator
class	DecomposeAndReweightEnergiesCalculator
class	EmptyVertexData
class	EnergiesData
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	SHOBuriedUnsatisfiedPolarsCalculator
class	SurfaceCalculator

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

Functions
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)
static thread_local basic::Tracer	TR ("seqrecovery")
static thread_local basic::Tracer	TR ("protocols.toolbox.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator")
void	residue_subset (std::string setf, utility::vector1< Size > &rset, core::pose::Pose &ps)
	extracts the pose indexes of a selected subset of residues More...

Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculator const > protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculatorCOP

typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculator > protocols::toolbox::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculatorOP

Function Documentation

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

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::residue_subset	(	std::string	setf,
		utility::vector1< Size > &	rset,
		core::pose::Pose &	ps
	)

extracts the pose indexes of a selected subset of residues

Parameters

[in]

setf

path to a file specifying the residue subset according to the following format:

C1 R1 I1
... CN RN IN
Here, Ci, Ri, and Ii indicate the chain identifier, residue index, and insertion code (as specified in the pose's input PDB file) of the ith residue in the subset (i=1,...,N; N>=1).

Parameters

[out]	rset	vector to hold the residue indexes. The vector must be passed empty.
[in]	ps	the pose.

: after this function has been called, rset[i] is the pose index of the residue specified by the ith input line (i=1,...,N).

: blank chain identifiers and insertion codes must be specified with the '_' character.

References core::pose::Pose::pdb_info(), and TR().

static thread_local basic::Tracer protocols::toolbox::pose_metric_calculators::TR ( "protocols.toolbox.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator"  )

static

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

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(), protocols::toolbox::pose_metric_calculators::FragQualCalculator::recompute(), and residue_subset().