protocols::pose_metric_calculators Namespace Reference

Classes
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	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
using	parent = core::pose::metrics::StructureDependentCalculator
using	one_group = std::set< core::Size >
typedef std::pair< one_group, one_group >	group_pair
using	group_set = utility::vector1< group_pair >
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 core::Real	RotamerProbability
typedef std::map< core::Size, RotamerProbability >	RotamerProbabilities
typedef utility::pointer::shared_ptr < SHOBuriedUnsatisfiedPolarsCalculator >	SHOBuriedUnsatisfiedPolarsCalculatorOP
typedef utility::pointer::shared_ptr < SHOBuriedUnsatisfiedPolarsCalculator const >	SHOBuriedUnsatisfiedPolarsCalculatorCOP

Functions
static basic::Tracer	TR ("protocols.toolbox.PoseMetricCalculators.ExplicitWaterUnsatisfiedPolarsCalculator")
void	append_rsd_by_jump_near_atom (pose::Pose &pose, core::Size seqpos, core::Size atomno, conformation::Residue new_rsd, core::Size new_atomno, Real dist_min, Real dist_max)
void	dock_waters_to_atom (pose::Pose &pose, ScoreFunctionOP scorefxn, core::Size seqpos, core::Size atomno, conformation::Residue wat_rsd, core::Size new_atomno, Real dist_min, Real dist_max)
void	find_res_unsat_polars (Pose const pose, core::Size const seqpos, vector1< bool > &atm_is_unsat)
core::Real	compute_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D< bool > const &subset)
bool	fast_clash_check (Pose const &pose, vector1< id::AtomID > const check_atids, Real const clash_dist_cut)
static basic::Tracer	TR ("seqrecovery")
static basic::Tracer	TR ("protocols.toolbox.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator")
void	residue_subset (std::string setf, utility::vector1< core::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::pose_metric_calculators::DecomposeAndReweightEnergiesCalculatorCOP

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

typedef std::pair< one_group, one_group > protocols::pose_metric_calculators::group_pair

using protocols::pose_metric_calculators::group_set = typedef utility::vector1<group_pair>

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

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

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

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

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

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

using protocols::pose_metric_calculators::one_group = typedef std::set<core::Size>

using protocols::pose_metric_calculators::parent = typedef core::pose::metrics::StructureDependentCalculator

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

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

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

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

typedef std::map< core::Size, RotamerProbability > protocols::pose_metric_calculators::RotamerProbabilities

typedef core::Real protocols::pose_metric_calculators::RotamerProbability

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

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

Function Documentation

void protocols::pose_metric_calculators::append_rsd_by_jump_near_atom	(	pose::Pose &	pose,
		core::Size	seqpos,
		core::Size	atomno,
		conformation::Residue	new_rsd,
		core::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(), core::scoring::rg, core::pose::Pose::set_jump(), and core::pose::Pose::size().

Referenced by dock_waters_to_atom().

core::Real protocols::pose_metric_calculators::compute_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		ObjexxFCL::FArray1D< bool > const &	subset
	)

References core::scoring::is_scatom(), and core::scoring::rmsd_no_super_subset().

Referenced by protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers().

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

References append_rsd_by_jump_near_atom(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::FoldTree::num_jump(), and core::pose::Pose::set_jump().

bool protocols::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::size(), and core::pose::Pose::xyz().

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

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

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

void protocols::pose_metric_calculators::residue_subset	(	std::string	setf,
		utility::vector1< core::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 basic::Tracer protocols::pose_metric_calculators::TR ( "protocols.toolbox.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator"  )

static

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

static

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

static

Referenced by protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::assert_calculators(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeAllBoltz(), protocols::pose_metric_calculators::SequenceComparison::fill_designable_set(), protocols::pose_metric_calculators::SequenceComparison::get_sequence_recovery(), protocols::pose_metric_calculators::FragQualCalculator::lookup(), protocols::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::pose_metric_calculators::FragQualCalculator::recompute(), and residue_subset().