Classes
class	CalculatorMetric
	A metric which can combine other metrics. More...

class	CalculatorMetricCreator

class	DihedralDistanceMetric
	A metric to calculate the dihedral distance between two poses. Can set a subset of residues to calculate via ResidueSelector. More...

class	DihedralDistanceMetricCreator

class	EXCN_CalcFailed
	Super-simple exception to be thrown when the SS calculator fails to compute. More...

class	EXCN_InitFailed
	Super-simple exception to be thrown when we can't initialize the SS calculator. 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	InteractionEnergyMetricCreator

class	ResidueSummaryMetric
	A SimpleMetric that takes a PerResidueRealMetric and calculates different summaries of the overall data. More...

class	ResidueSummaryMetricCreator

class	RMSDMetric
	A metric to calculate the RMSD between two poses. Can set a subset of residues to calculate via ResidueSelector. More...

class	RMSDMetricCreator

class	SasaMetric
	A Metric to cacluate overall sasa of a pose. More...

class	SasaMetricCreator

class	SecondaryStructureMetric
	A SimpleMetric to output the secondary structure of the protein or residues selected by a residue selector. Uses DSSP. More...

class	SecondaryStructureMetricCreator

class	SelectedResidueCountMetric
	A SimpleMetric that counts the number of residues in a residue selection. More...

class	SelectedResidueCountMetricCreator

class	SelectedResiduesMetric
	Output residue-selected residues to a score file as rosetta resnums or pdbnums. More...

class	SelectedResiduesMetricCreator

class	SelectedResiduesPyMOLMetric
	A utility metric to output a string of selected residues from a residue selector as a pymol selection. More...

class	SelectedResiduesPyMOLMetricCreator

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	SequenceMetricCreator

class	SequenceSimilarityMetric
	compares the sequences of the native structure (using native flag) to the sequence of a given pose using BLOSUM 62. More...

class	SequenceSimilarityMetricCreator

class	ShapeSimilarityMetric

class	ShapeSimilarityMetricCreator

class	TimingProfileMetric
	Calculate the time difference between construction and apply/calculate. Useful to time protocols in RosettaScripts or through mover containers. More...

class	TimingProfileMetricCreator

class	TotalEnergyMetric
	A metric to report the total energy of the system or the delta total energy between another input pose. More...

class	TotalEnergyMetricCreator

Typedefs
using	CalculatorMetricOP = utility::pointer::shared_ptr< CalculatorMetric >

using	CalculatorMetricCOP = utility::pointer::shared_ptr< CalculatorMetric const >

typedef utility::pointer::shared_ptr < DihedralDistanceMetric >	DihedralDistanceMetricOP

typedef utility::pointer::shared_ptr < DihedralDistanceMetric const >	DihedralDistanceMetricCOP

typedef utility::pointer::shared_ptr < InteractionEnergyMetric >	InteractionEnergyMetricOP

typedef utility::pointer::shared_ptr < InteractionEnergyMetric const >	InteractionEnergyMetricCOP

typedef utility::pointer::shared_ptr < ResidueSummaryMetric >	ResidueSummaryMetricOP

typedef utility::pointer::shared_ptr < ResidueSummaryMetric const >	ResidueSummaryMetricCOP

typedef utility::pointer::shared_ptr < RMSDMetric >	RMSDMetricOP

typedef utility::pointer::shared_ptr < RMSDMetric const >	RMSDMetricCOP

typedef utility::pointer::shared_ptr < SasaMetric >	SasaMetricOP

typedef utility::pointer::shared_ptr < SasaMetric const >	SasaMetricCOP

typedef utility::pointer::shared_ptr < SecondaryStructureMetric >	SecondaryStructureMetricOP

typedef utility::pointer::shared_ptr < SecondaryStructureMetric const >	SecondaryStructureMetricCOP

typedef utility::pointer::shared_ptr < SelectedResidueCountMetric >	SelectedResidueCountMetricOP

typedef utility::pointer::shared_ptr < SelectedResidueCountMetric const >	SelectedResidueCountMetricCOP

typedef utility::pointer::shared_ptr < SelectedResiduesMetric >	SelectedResiduesMetricOP

typedef utility::pointer::shared_ptr < SelectedResiduesMetric const >	SelectedResiduesMetricCOP

typedef utility::pointer::shared_ptr < SelectedResiduesPyMOLMetric >	SelectedResiduesPyMOLMetricOP

typedef utility::pointer::shared_ptr < SelectedResiduesPyMOLMetric const >	SelectedResiduesPyMOLMetricCOP

typedef utility::pointer::shared_ptr < SequenceMetric >	SequenceMetricOP

typedef utility::pointer::shared_ptr < SequenceMetric const >	SequenceMetricCOP

typedef utility::pointer::shared_ptr < SequenceSimilarityMetric >	SequenceSimilarityMetricOP

typedef utility::pointer::shared_ptr < SequenceSimilarityMetric const >	SequenceSimilarityMetricCOP

typedef utility::pointer::shared_ptr < ShapeSimilarityMetric >	ShapeSimilarityMetricOP

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 < TimingProfileMetric >	TimingProfileMetricOP

typedef utility::pointer::shared_ptr < TimingProfileMetric const >	TimingProfileMetricCOP

typedef utility::pointer::shared_ptr < TotalEnergyMetric >	TotalEnergyMetricOP

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	SequenceMetricMode { SMM_ONELETTER_CODE =1, SMM_THREELETTER_CODE, SMM_BASE_NAME, SMM_FULL_NAME, SMM_INVALID_MODE, SMM_END_OF_LIST = SMM_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_type >	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 const std::map < SequenceMetricMode, std::string >	mode_to_name_map_ ({{SMM_ONELETTER_CODE,"oneletter"},{SMM_THREELETTER_CODE,"threeletter"},{SMM_BASE_NAME,"basename"},{SMM_FULL_NAME,"fullname"},{SMM_INVALID_MODE,"INVALID"}})
	The map of enum to name. More...

Typedef Documentation

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

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

typedef utility::pointer::shared_ptr< DihedralDistanceMetric const > core::simple_metrics::metrics::DihedralDistanceMetricCOP

typedef utility::pointer::shared_ptr< DihedralDistanceMetric > core::simple_metrics::metrics::DihedralDistanceMetricOP

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

typedef utility::pointer::shared_ptr< InteractionEnergyMetric const > core::simple_metrics::metrics::InteractionEnergyMetricCOP

typedef utility::pointer::shared_ptr< InteractionEnergyMetric > core::simple_metrics::metrics::InteractionEnergyMetricOP

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

typedef utility::pointer::shared_ptr< ResidueSummaryMetric const > core::simple_metrics::metrics::ResidueSummaryMetricCOP

typedef utility::pointer::shared_ptr< ResidueSummaryMetric > core::simple_metrics::metrics::ResidueSummaryMetricOP

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

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

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

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

typedef utility::pointer::shared_ptr< SecondaryStructureMetric const > core::simple_metrics::metrics::SecondaryStructureMetricCOP

typedef utility::pointer::shared_ptr< SecondaryStructureMetric > core::simple_metrics::metrics::SecondaryStructureMetricOP

typedef utility::pointer::shared_ptr< SelectedResidueCountMetric const > core::simple_metrics::metrics::SelectedResidueCountMetricCOP

typedef utility::pointer::shared_ptr< SelectedResidueCountMetric > core::simple_metrics::metrics::SelectedResidueCountMetricOP

typedef utility::pointer::shared_ptr< SelectedResiduesMetric const > core::simple_metrics::metrics::SelectedResiduesMetricCOP

typedef utility::pointer::shared_ptr< SelectedResiduesMetric > core::simple_metrics::metrics::SelectedResiduesMetricOP

typedef utility::pointer::shared_ptr< SelectedResiduesPyMOLMetric const > core::simple_metrics::metrics::SelectedResiduesPyMOLMetricCOP

typedef utility::pointer::shared_ptr< SelectedResiduesPyMOLMetric > core::simple_metrics::metrics::SelectedResiduesPyMOLMetricOP

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

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

typedef utility::pointer::shared_ptr< SequenceSimilarityMetric const > core::simple_metrics::metrics::SequenceSimilarityMetricCOP

typedef utility::pointer::shared_ptr< SequenceSimilarityMetric > core::simple_metrics::metrics::SequenceSimilarityMetricOP

typedef utility::pointer::shared_ptr< ShapeSimilarityMetric const > core::simple_metrics::metrics::ShapeSimilarityMetricCOP

typedef utility::pointer::shared_ptr< ShapeSimilarityMetric > core::simple_metrics::metrics::ShapeSimilarityMetricOP

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

typedef utility::pointer::shared_ptr< TimingProfileMetric > core::simple_metrics::metrics::TimingProfileMetricOP

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

typedef utility::pointer::shared_ptr< TotalEnergyMetric > core::simple_metrics::metrics::TotalEnergyMetricOP

Enumeration Type Documentation

enum core::simple_metrics::metrics::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
SMM_ONELETTER_CODE
SMM_THREELETTER_CODE
SMM_BASE_NAME
SMM_FULL_NAME
SMM_INVALID_MODE
SMM_END_OF_LIST

enum core::simple_metrics::metrics::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

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

References summary_string_to_type().

Referenced by core::simple_metrics::metrics::ResidueSummaryMetric::provide_xml_schema().

static const std::map< SequenceMetricMode, std::string > core::simple_metrics::metrics::mode_to_name_map_ ( {{SMM_ONELETTER_CODE,"oneletter"},{SMM_THREELETTER_CODE,"threeletter"},{SMM_BASE_NAME,"basename"},{SMM_FULL_NAME,"fullname"},{SMM_INVALID_MODE,"INVALID"}} )

static

The map of enum to name.

Referenced by core::simple_metrics::metrics::SequenceMetric::mode_name_from_enum().

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

Referenced by get_summary_type_strings(), and core::simple_metrics::metrics::ResidueSummaryMetric::parse_my_tag().

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation