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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

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

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 
)
core::Real protocols::pose_metric_calculators::compute_rmsd ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2,
ObjexxFCL::FArray1D< bool > const &  subset 
)
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 
)
bool protocols::pose_metric_calculators::fast_clash_check ( Pose const &  pose,
vector1< id::AtomID > const  check_atids,
Real const  clash_dist_cut 
)
void protocols::pose_metric_calculators::find_res_unsat_polars ( Pose const  pose,
core::Size const  seqpos,
vector1< bool > &  atm_is_unsat 
)
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().

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