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core::simple_metrics::metrics Namespace Reference

Classes

class  CalculatorMetric
 A metric which can combine other metrics. More...
 
class  CalculatorMetricCreator
 
class  CustomRealValueMetric
 A simple metric that allows an arbitrary, user- or developer-set floating-point value to be cached in a pose. More...
 
class  CustomRealValueMetricCreator
 
class  CustomStringValueMetric
 A simple metric that allows an arbitrary, user- or developer-set string to be cached in a pose. More...
 
class  CustomStringValueMetricCreator
 
class  DihedralDistanceMetric
 A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector. More...
 
class  InteractionEnergyMetric
 Calculate the interaction energy between residues in two ResidueSelectors in a single pose, including long-range interactions. Pose should be scored! More...
 
class  ResidueSummaryMetric
 A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data. More...
 
class  RMSDMetric
 A metric to calculate the RMSD between two poses. Can set a subset of residues to calculate via ResidueSelector. More...
 
class  SasaMetric
 A Metric to cacluate overall sasa of a pose. More...
 
class  SecondaryStructureMetric
 A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP. More...
 
class  SelectedResidueCountMetric
 A SimpleMetric that counts the number of residues in a residue selection. More...
 
class  SelectedResiduesMetric
 Output residue-selected residues to a score file as rosetta resnums or pdbnums. More...
 
class  SelectedResiduesPyMOLMetric
 A utility metric to output a string of selected residues from a residue selector as a pymol selection. More...
 
class  SequenceMetric
 A SimpleMetric to output the single-letter OR three-letter sequence of a protein or subset of positions/regions using a ResidueSelector. More...
 
class  SequenceSimilarityMetric
 compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62. More...
 
class  ShapeSimilarityMetric
 
class  EXCN_InitFailed
 Super-simple exception to be thrown when we can't initialize the SS calculator. More...
 
class  EXCN_CalcFailed
 Super-simple exception to be thrown when the SS calculator fails to compute. More...
 
class  TimingProfileMetric
 Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers. More...
 
class  TotalEnergyMetric
 A metric to report the total energy of the system or the delta total energy between another input pose. More...
 
class  DihedralDistanceMetricCreator
 
class  InteractionEnergyMetricCreator
 
class  ResidueSummaryMetricCreator
 
class  RMSDMetricCreator
 
class  SasaMetricCreator
 
class  SecondaryStructureMetricCreator
 
class  SelectedResidueCountMetricCreator
 
class  SelectedResiduesMetricCreator
 
class  SelectedResiduesPyMOLMetricCreator
 
class  SequenceMetricCreator
 
class  SequenceSimilarityMetricCreator
 
class  TimingProfileMetricCreator
 
class  TotalEnergyMetricCreator
 
class  ShapeSimilarityMetricCreator
 

Typedefs

using CalculatorMetricOP = utility::pointer::shared_ptr< CalculatorMetric >
 
using CalculatorMetricCOP = utility::pointer::shared_ptr< CalculatorMetric const >
 
typedef utility::pointer::shared_ptr< CustomRealValueMetricCustomRealValueMetricOP
 
typedef utility::pointer::shared_ptr< CustomRealValueMetric const > CustomRealValueMetricCOP
 
typedef utility::pointer::shared_ptr< CustomStringValueMetricCustomStringValueMetricOP
 
typedef utility::pointer::shared_ptr< CustomStringValueMetric const > CustomStringValueMetricCOP
 
typedef utility::pointer::shared_ptr< DihedralDistanceMetricDihedralDistanceMetricOP
 
typedef utility::pointer::shared_ptr< DihedralDistanceMetric const > DihedralDistanceMetricCOP
 
typedef utility::pointer::shared_ptr< InteractionEnergyMetricInteractionEnergyMetricOP
 
typedef utility::pointer::shared_ptr< InteractionEnergyMetric const > InteractionEnergyMetricCOP
 
typedef utility::pointer::shared_ptr< ResidueSummaryMetricResidueSummaryMetricOP
 
typedef utility::pointer::shared_ptr< ResidueSummaryMetric const > ResidueSummaryMetricCOP
 
typedef utility::pointer::shared_ptr< RMSDMetricRMSDMetricOP
 
typedef utility::pointer::shared_ptr< RMSDMetric const > RMSDMetricCOP
 
typedef utility::pointer::shared_ptr< SasaMetricSasaMetricOP
 
typedef utility::pointer::shared_ptr< SasaMetric const > SasaMetricCOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureMetricSecondaryStructureMetricOP
 
typedef utility::pointer::shared_ptr< SecondaryStructureMetric const > SecondaryStructureMetricCOP
 
typedef utility::pointer::shared_ptr< SelectedResidueCountMetricSelectedResidueCountMetricOP
 
typedef utility::pointer::shared_ptr< SelectedResidueCountMetric const > SelectedResidueCountMetricCOP
 
typedef utility::pointer::shared_ptr< SelectedResiduesMetricSelectedResiduesMetricOP
 
typedef utility::pointer::shared_ptr< SelectedResiduesMetric const > SelectedResiduesMetricCOP
 
typedef utility::pointer::shared_ptr< SelectedResiduesPyMOLMetricSelectedResiduesPyMOLMetricOP
 
typedef utility::pointer::shared_ptr< SelectedResiduesPyMOLMetric const > SelectedResiduesPyMOLMetricCOP
 
typedef utility::pointer::shared_ptr< SequenceMetricSequenceMetricOP
 
typedef utility::pointer::shared_ptr< SequenceMetric const > SequenceMetricCOP
 
typedef utility::pointer::shared_ptr< SequenceSimilarityMetricSequenceSimilarityMetricOP
 
typedef utility::pointer::shared_ptr< SequenceSimilarityMetric const > SequenceSimilarityMetricCOP
 
typedef utility::pointer::shared_ptr< ShapeSimilarityMetricShapeSimilarityMetricOP
 
typedef utility::pointer::shared_ptr< ShapeSimilarityMetric const > ShapeSimilarityMetricCOP
 
using minutes_timing = duration< float, std::ratio< 60, 1 > >
 
using hours_timing = duration< float, std::ratio< 3600, 1 > >
 
typedef utility::pointer::shared_ptr< TimingProfileMetricTimingProfileMetricOP
 
typedef utility::pointer::shared_ptr< TimingProfileMetric const > TimingProfileMetricCOP
 
typedef utility::pointer::shared_ptr< TotalEnergyMetricTotalEnergyMetricOP
 
typedef utility::pointer::shared_ptr< TotalEnergyMetric const > TotalEnergyMetricCOP
 

Enumerations

enum  summary_type {
  sum = 1 , mean , n_res_eq , n_res_ne ,
  n_res_gt , n_res_lt , n_res_gt_or_eq , n_res_lt_or_eq ,
  bogus , summary_type_total = bogus
}
 Enum that tells us HOW to summarize the PerResidueMetric data. More...
 
enum class  SequenceMetricMode {
  ONELETTER_CODE =1 , THREELETTER_CODE , BASE_NAME , FULL_NAME ,
  INVALID_MODE , END_OF_LIST = INVALID_MODE
}
 The mode for this metric. If you add to this list, be sure to update the map associating this enum with corresponding strings in the .cc file. More...
 

Functions

utility::vector1< std::string > get_summary_type_strings ()
 
static const std::map< std::string, summary_typesummary_string_to_type ({ { "sum", sum }, { "mean", mean }, { "n_res_eq", n_res_eq }, { "n_res_ne", n_res_ne }, { "n_res_lt", n_res_lt }, { "n_res_gt", n_res_gt }, { "n_res_lt_or_eq", n_res_lt_or_eq }, { "n_res_gt_or_eq", n_res_gt_or_eq } })
 
static const std::map< SequenceMetricMode, std::string > mode_to_name_map_ ({ { SequenceMetricMode::ONELETTER_CODE, "oneletter" }, { SequenceMetricMode::THREELETTER_CODE, "threeletter" }, { SequenceMetricMode::BASE_NAME, "basename" }, { SequenceMetricMode::FULL_NAME, "fullname" }, { SequenceMetricMode::INVALID_MODE, "INVALID" } })
 The map of enum to name. More...
 

Typedef Documentation

◆ CalculatorMetricCOP

using core::simple_metrics::metrics::CalculatorMetricCOP = typedef utility::pointer::shared_ptr< CalculatorMetric const >

◆ CalculatorMetricOP

using core::simple_metrics::metrics::CalculatorMetricOP = typedef utility::pointer::shared_ptr< CalculatorMetric >

◆ CustomRealValueMetricCOP

◆ CustomRealValueMetricOP

◆ CustomStringValueMetricCOP

◆ CustomStringValueMetricOP

◆ DihedralDistanceMetricCOP

◆ DihedralDistanceMetricOP

◆ hours_timing

using core::simple_metrics::metrics::hours_timing = typedef duration< float, std::ratio< 3600, 1> >

◆ InteractionEnergyMetricCOP

◆ InteractionEnergyMetricOP

◆ minutes_timing

using core::simple_metrics::metrics::minutes_timing = typedef duration< float, std::ratio< 60, 1 > >

◆ ResidueSummaryMetricCOP

◆ ResidueSummaryMetricOP

◆ RMSDMetricCOP

typedef utility::pointer::shared_ptr< RMSDMetric const > core::simple_metrics::metrics::RMSDMetricCOP

◆ RMSDMetricOP

typedef utility::pointer::shared_ptr< RMSDMetric > core::simple_metrics::metrics::RMSDMetricOP

◆ SasaMetricCOP

typedef utility::pointer::shared_ptr< SasaMetric const > core::simple_metrics::metrics::SasaMetricCOP

◆ SasaMetricOP

typedef utility::pointer::shared_ptr< SasaMetric > core::simple_metrics::metrics::SasaMetricOP

◆ SecondaryStructureMetricCOP

◆ SecondaryStructureMetricOP

◆ SelectedResidueCountMetricCOP

◆ SelectedResidueCountMetricOP

◆ SelectedResiduesMetricCOP

◆ SelectedResiduesMetricOP

◆ SelectedResiduesPyMOLMetricCOP

◆ SelectedResiduesPyMOLMetricOP

◆ SequenceMetricCOP

typedef utility::pointer::shared_ptr< SequenceMetric const > core::simple_metrics::metrics::SequenceMetricCOP

◆ SequenceMetricOP

typedef utility::pointer::shared_ptr< SequenceMetric > core::simple_metrics::metrics::SequenceMetricOP

◆ SequenceSimilarityMetricCOP

◆ SequenceSimilarityMetricOP

◆ ShapeSimilarityMetricCOP

◆ ShapeSimilarityMetricOP

◆ TimingProfileMetricCOP

typedef utility::pointer::shared_ptr< TimingProfileMetric const > core::simple_metrics::metrics::TimingProfileMetricCOP

◆ TimingProfileMetricOP

◆ TotalEnergyMetricCOP

typedef utility::pointer::shared_ptr< TotalEnergyMetric const > core::simple_metrics::metrics::TotalEnergyMetricCOP

◆ TotalEnergyMetricOP

Enumeration Type Documentation

◆ SequenceMetricMode

The mode for this metric. If you add to this list, be sure to update the map associating this enum with corresponding strings in the .cc file.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)
Enumerator
ONELETTER_CODE 
THREELETTER_CODE 
BASE_NAME 
FULL_NAME 
INVALID_MODE 
END_OF_LIST 

◆ summary_type

Enum that tells us HOW to summarize the PerResidueMetric data.

Enumerator
sum 
mean 
n_res_eq 
n_res_ne 
n_res_gt 
n_res_lt 
n_res_gt_or_eq 
n_res_lt_or_eq 
bogus 
summary_type_total 

Function Documentation

◆ get_summary_type_strings()

utility::vector1< std::string > core::simple_metrics::metrics::get_summary_type_strings ( )

◆ mode_to_name_map_()

static const std::map< SequenceMetricMode, std::string > core::simple_metrics::metrics::mode_to_name_map_ ( { { SequenceMetricMode::ONELETTER_CODE, "oneletter" }, { SequenceMetricMode::THREELETTER_CODE, "threeletter" }, { SequenceMetricMode::BASE_NAME, "basename" }, { SequenceMetricMode::FULL_NAME, "fullname" }, { SequenceMetricMode::INVALID_MODE, "INVALID" } }  )
static

◆ summary_string_to_type()

static const std::map< std::string, summary_type > core::simple_metrics::metrics::summary_string_to_type ( { { "sum", sum }, { "mean", mean }, { "n_res_eq", n_res_eq }, { "n_res_ne", n_res_ne }, { "n_res_lt", n_res_lt }, { "n_res_gt", n_res_gt }, { "n_res_lt_or_eq", n_res_lt_or_eq }, { "n_res_gt_or_eq", n_res_gt_or_eq } }  )
static