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Classes | Typedefs | Functions
protocols::pose_metric_calculators Namespace Reference

Classes

class  CatPiCalculator
 
class  ChargeCalculator
 
class  ClashCountCalculator
 
class  EnergiesData
 
class  EmptyVertexData
 
class  DecomposeAndReweightEnergiesCalculator
 
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< DecomposeAndReweightEnergiesCalculatorDecomposeAndReweightEnergiesCalculatorOP
 
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_groupgroup_pair
 
using group_set = utility::vector1< group_pair >
 
typedef utility::pointer::shared_ptr< InterGroupNeighborsCalculatorInterGroupNeighborsCalculatorOP
 
typedef utility::pointer::shared_ptr< InterGroupNeighborsCalculator const > InterGroupNeighborsCalculatorCOP
 
typedef utility::pointer::shared_ptr< NeighborhoodByDistanceCalculatorNeighborhoodByDistanceCalculatorOP
 
typedef utility::pointer::shared_ptr< NeighborhoodByDistanceCalculator const > NeighborhoodByDistanceCalculatorCOP
 
typedef utility::pointer::shared_ptr< NeighborsByDistanceCalculatorNeighborsByDistanceCalculatorOP
 
typedef utility::pointer::shared_ptr< NeighborsByDistanceCalculator const > NeighborsByDistanceCalculatorCOP
 
typedef utility::pointer::shared_ptr< ResidueDecompositionByChainCalculatorResidueDecompositionByChainCalculatorOP
 
typedef utility::pointer::shared_ptr< ResidueDecompositionByChainCalculator const > ResidueDecompositionByChainCalculatorCOP
 
typedef utility::pointer::shared_ptr< RotamerBoltzCalculatorRotamerBoltzCalculatorOP
 
typedef utility::pointer::shared_ptr< RotamerBoltzCalculator const > RotamerBoltzCalculatorCOP
 
typedef core::Real RotamerProbability
 
typedef std::map< core::Size, RotamerProbabilityRotamerProbabilities
 
typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculatorSHOBuriedUnsatisfiedPolarsCalculatorOP
 
typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculator const > SHOBuriedUnsatisfiedPolarsCalculatorCOP
 

Functions

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

◆ DecomposeAndReweightEnergiesCalculatorCOP

◆ DecomposeAndReweightEnergiesCalculatorOP

◆ group_pair

◆ group_set

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

◆ InterGroupNeighborsCalculatorCOP

◆ InterGroupNeighborsCalculatorOP

◆ NeighborhoodByDistanceCalculatorCOP

◆ NeighborhoodByDistanceCalculatorOP

◆ NeighborsByDistanceCalculatorCOP

◆ NeighborsByDistanceCalculatorOP

◆ one_group

◆ parent

◆ ResidueDecompositionByChainCalculatorCOP

◆ ResidueDecompositionByChainCalculatorOP

◆ RotamerBoltzCalculatorCOP

◆ RotamerBoltzCalculatorOP

◆ RotamerProbabilities

◆ RotamerProbability

◆ SHOBuriedUnsatisfiedPolarsCalculatorCOP

◆ SHOBuriedUnsatisfiedPolarsCalculatorOP

Function Documentation

◆ compute_rmsd()

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

◆ fast_clash_check()

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

◆ residue_subset()

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]setfpath 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]rsetvector to hold the residue indexes. The vector must be passed empty.
[in]psthe 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().

Referenced by protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two(), and protocols::backrub::BackrubProtocol::set_pivots_from_residue_subset().

◆ TR() [1/2]

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

◆ TR() [2/2]

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