A simple metric for measuring the backbone hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds. More...

#include <PeptideInternalHbondsMetric.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideInternalHbondsMetric:

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Public Member Functions
	PeptideInternalHbondsMetric ()=default
	Constructors ///. More...

	PeptideInternalHbondsMetric (PeptideInternalHbondsMetric const &)=default
	Copy constructor (not needed unless you need deep copies) More...

	~PeptideInternalHbondsMetric () override=default
	Destructor (important for properly forward-declaring smart-pointer members) More...

core::simple_metrics::SimpleMetricOP	clone () const override
	Duplicate this object, and return a smart pointer to the copy. More...

core::Real	calculate (core::pose::Pose const &pose) const override
	Metric Methods ///. More...

std::string	name () const override
	Name of the class. More...

std::string	metric () const override
	Return text indicating what we're measuring. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	called by parse_my_tag – should not be used directly More...

void	configure_from_filter_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data)
	Configure this metric from the tag passed to the companion filter (the PeptideInternalHbondsFilter). More...

void	report (std::ostream &outstream, core::pose::Pose const &pose) const
	allows printing data to a stream. More...

void	set_hbond_types (bool const backbone_backbone_setting, bool const backbone_sidechain_setting, bool const sidechain_sidechain_setting)
	Set whether we're counting backbone-backbone, backbone-sidechain, and sidechain-sidechain hydrogen bonds. More...

void	set_exclusion_distance (core::Size const setting)
	Set the number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted. More...

void	set_hbond_energy_cutoff (core::Real const setting)
	Set the energy cutoff for counting a hydrogen bond. More...

void	set_scorefxn (core::scoring::ScoreFunctionCOP const &sfxn_in)
	Set the scorefunction for identifying hydrogen bonds. If this is not called, the default scorefunction is used. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP const &res_selector_in)
	Set the scorefunction for selecting the peptide. If this is not called, whole pose is counted. More...

bool	backbone_backbone () const
	Get whether we're counting backbone-backbone hbonds: More...

bool	backbone_sidechain () const
	Get whether we're counting backbone-sidechain hbonds: More...

bool	sidechain_sidechain () const
	Get whether we're counting sidechain-sidechain hbonds: More...

core::Size	exclusion_distance () const
	Get the number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted. More...

core::Real	hbond_energy_cutoff () const
	Get the energy cutoff for counting a hydrogen bond. More...

core::scoring::ScoreFunctionCOP	scorefxn () const
	Get the scorefunction for identifying hydrogen bonds. Note that if this is nullptr, the default scorefunction is used. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector () const
	Get the scorefunction for selecting the peptide. If this nullptr, whole pose is counted. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from core::simple_metrics::RealMetric
	RealMetric ()

	~RealMetric () override

	RealMetric (RealMetric const &other)

RealMetric &	operator= (RealMetric const &)

void	apply (std::string const &out_label, pose::Pose &pose, bool override_existing_data=false) const override
	Calculate the metric and add it to the pose as a score. labeled as out_label. More...

core::Real	cached_calculate (pose::Pose const &pose, bool use_cache, std::string prefix="", std::string suffix="", bool fail_on_missing_cache=true) const
	Grab the data from the pose if it exists or calculate the metric. More...

utility::vector1< std::string >	get_metric_names () const override
	Get the metric name(s) that this Metric will calculate. More...

Public Member Functions inherited from core::simple_metrics::SimpleMetric
	SimpleMetric (std::string const &simple_metric_type)

	~SimpleMetric () override

	SimpleMetric (SimpleMetric const &other)

SimpleMetric &	operator= (SimpleMetric const &)

void	apply (pose::Pose &pose, std::string const &prefix="", std::string const &suffix="", bool override_existing_data=false) const
	Calculate the metric and add it to the Score, which is output into a scorefile - labeled as prefix+metric+suffix. More...

void	set_custom_type (std::string const &custom_type)

std::string	get_custom_type () const
	Additional setting to prefix/suffix. More...

virtual void	parse_base_tag (utility::tag::TagCOP tag)
	Parse the base class tag. Keep required interface for parse_my_tag. More...

std::string	simple_metric_type () const

std::string	get_final_sm_type () const
	Get the final name of this metric including its simple_metric_type_ name and any set custom type. More...

Static Public Member Functions
static std::string	name_static ()
	Name of the class for creator. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Provide a description of the XML interface. More...

static void	provide_shared_xml_schema_elements (utility::tag::AttributeList &attlist)
	Provide descriptions of XML interface elements shared between this metric and the companion filter. More...

Static Public Member Functions inherited from core::simple_metrics::SimpleMetric
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_simple_metric (utility::tag::XMLSchemaDefinition &)

Private Member Functions
core::Size	count_hbonds (core::pose::Pose const &original_pose, core::select::residue_selector::ResidueSubset const &selection) const
	Given a pose and a selection, count the internal hydrogen bonds. More...

utility::vector1< std::list < core::Size > >	generate_allowed_partners (core::pose::Pose const &pose, utility::vector1< core::Size > const &selected_residues) const
	Given a vector of selected resiudes and a pose, construct a vector of lists of allowed residue partners. More...

Private Attributes
bool	backbone_backbone_ = true
	Are we counting backbone-backbone hydrogen bonds? Default true. More...

bool	backbone_sidechain_ = false
	Are we counting backbone-sidechain hydrogen bonds? Default false. More...

bool	sidechain_sidechain_ = false
	Are we counting sidechain-sidechain hydrogen bonds? Default false. More...

core::Size	exclusion_distance_ = 1
	The number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted. Defaults to 1. More...

core::Real	hbond_energy_cutoff_ = -0.25
	The energy cutoff for counting a hydrogen bond. Defaults to -0.25. More...

core::scoring::ScoreFunctionCOP	scorefxn_
	The scorefunction to use for evaluating hydrogen bonds. If none is provided, we'll grab the default scorefunction and cache it. More...

core::select::residue_selector::ResidueSelectorCOP	residue_selector_
	The residue selector. If none is provided, we evaluate the whole pose. More...

Friends
class	::PeptideInternalHbondsMetricTests

Detailed Description

A simple metric for measuring the backbone hydrogen bonds within a peptide backbone, ignoring hydrogen bonds to other parts of a pose. Note that this metric does not count intra-residue hydrogen bonds.

Constructor & Destructor Documentation

protocols::cyclic_peptide::PeptideInternalHbondsMetric::PeptideInternalHbondsMetric ( )

default

Constructors ///.

Default constructor

protocols::cyclic_peptide::PeptideInternalHbondsMetric::PeptideInternalHbondsMetric ( PeptideInternalHbondsMetric const & )

default

Copy constructor (not needed unless you need deep copies)

protocols::cyclic_peptide::PeptideInternalHbondsMetric::~PeptideInternalHbondsMetric ( )

overridedefault

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_backbone ( ) const

inline

Get whether we're counting backbone-backbone hbonds:

References backbone_backbone_.

Referenced by configure_from_filter_tag(), and count_hbonds().

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_sidechain ( ) const

inline

Get whether we're counting backbone-sidechain hbonds:

References backbone_sidechain_.

Referenced by configure_from_filter_tag(), and count_hbonds().

core::Real protocols::cyclic_peptide::PeptideInternalHbondsMetric::calculate ( core::pose::Pose const & pose ) const

overridevirtual

Metric Methods ///.

Calculate the metric.

Defined in RealMetric:

Calculate the metric and add it to the pose as a score. labeled as prefix+metric+suffix.

Score is added through setExtraScorePose and is output into the score tables/file at pose output. Calculate the metric.

Implements core::simple_metrics::RealMetric.

References count_hbonds(), residue_selector_, core::pose::Pose::total_residue(), and protocols::cyclic_peptide::TR().

core::simple_metrics::SimpleMetricOP protocols::cyclic_peptide::PeptideInternalHbondsMetric::clone ( ) const

overridevirtual

Duplicate this object, and return a smart pointer to the copy.

Implements core::simple_metrics::RealMetric.

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::configure_from_filter_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

Configure this metric from the tag passed to the companion filter (the PeptideInternalHbondsFilter).

References backbone_backbone(), backbone_sidechain(), exclusion_distance(), hbond_energy_cutoff(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), set_exclusion_distance(), set_hbond_energy_cutoff(), set_hbond_types(), set_residue_selector(), set_scorefxn(), and sidechain_sidechain().

Referenced by parse_my_tag().

core::Size protocols::cyclic_peptide::PeptideInternalHbondsMetric::count_hbonds	(	core::pose::Pose const &	original_pose,
		core::select::residue_selector::ResidueSubset const &	selection
	)		const

private

core::Size protocols::cyclic_peptide::PeptideInternalHbondsMetric::exclusion_distance ( ) const

inline

Get the number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted.

Defaults to 1.

References exclusion_distance_.

Referenced by configure_from_filter_tag(), and generate_allowed_partners().

utility::vector1< std::list< core::Size > > protocols::cyclic_peptide::PeptideInternalHbondsMetric::generate_allowed_partners	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size > const &	selected_residues
	)		const

private

Given a vector of selected resiudes and a pose, construct a vector of lists of allowed residue partners.

This is an O(N^2) operation, unfortunately. However, the selected_residues list should be small, and N is its length.

References exclusion_distance(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by count_hbonds().

core::Real protocols::cyclic_peptide::PeptideInternalHbondsMetric::hbond_energy_cutoff ( ) const

inline

Get the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

References hbond_energy_cutoff_.

Referenced by configure_from_filter_tag().

std::string protocols::cyclic_peptide::PeptideInternalHbondsMetric::metric ( ) const

overridevirtual

Return text indicating what we're measuring.

Implements core::simple_metrics::RealMetric.

std::string protocols::cyclic_peptide::PeptideInternalHbondsMetric::name ( ) const

overridevirtual

Name of the class.

Implements core::simple_metrics::RealMetric.

References name_static().

std::string protocols::cyclic_peptide::PeptideInternalHbondsMetric::name_static ( )

static

Name of the class for creator.

Referenced by protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::keyname(), name(), provide_citation_info(), and provide_xml_schema().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

called by parse_my_tag – should not be used directly

Implements core::simple_metrics::RealMetric.

References configure_from_filter_tag().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from core::simple_metrics::SimpleMetric.

References name_static(), residue_selector_, and scorefxn_.

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements ( utility::tag::AttributeList & attlist )

static

Provide descriptions of XML interface elements shared between this metric and the companion filter.

Provide XML interface elements shared between this metric and the companion filter.

References core::select::residue_selector::attributes_for_parse_residue_selector(), and core::scoring::attributes_for_parse_score_function_w_description().

Referenced by protocols::cyclic_peptide::PeptideInternalHbondsFilter::provide_xml_schema(), and provide_xml_schema().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

Provide a description of the XML interface.

References name_static(), provide_shared_xml_schema_elements(), and core::simple_metrics::xsd_simple_metric_type_definition_w_attributes().

Referenced by protocols::cyclic_peptide::PeptideInternalHbondsMetricCreator::provide_xml_schema().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::report	(	std::ostream &	outstream,
		core::pose::Pose const &	pose
	)		const

allows printing data to a stream.

References count_hbonds(), residue_selector_, and core::pose::Pose::total_residue().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::PeptideInternalHbondsMetric::residue_selector ( ) const

inline

Get the scorefunction for selecting the peptide. If this nullptr, whole pose is counted.

References residue_selector_.

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::PeptideInternalHbondsMetric::scorefxn ( ) const

inline

Get the scorefunction for identifying hydrogen bonds. Note that if this is nullptr, the default scorefunction is used.

References scorefxn_.

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_exclusion_distance ( core::Size const setting )

Set the number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted.

Defaults to 1.

References exclusion_distance_.

Referenced by configure_from_filter_tag().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_hbond_energy_cutoff ( core::Real const setting )

Set the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

References hbond_energy_cutoff_.

Referenced by configure_from_filter_tag().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_hbond_types	(	bool const	backbone_backbone_setting,
		bool const	backbone_sidechain_setting,
		bool const	sidechain_sidechain_setting
	)

Set whether we're counting backbone-backbone, backbone-sidechain, and sidechain-sidechain hydrogen bonds.

Throws if all are set to false. Defaults to only backbone-backbone being true.

References backbone_backbone_, backbone_sidechain_, and sidechain_sidechain_.

Referenced by configure_from_filter_tag().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP const & res_selector_in )

Set the scorefunction for selecting the peptide. If this is not called, whole pose is counted.

References residue_selector_.

Referenced by configure_from_filter_tag().

void protocols::cyclic_peptide::PeptideInternalHbondsMetric::set_scorefxn ( core::scoring::ScoreFunctionCOP const & sfxn_in )

Set the scorefunction for identifying hydrogen bonds. If this is not called, the default scorefunction is used.

References scorefxn_.

Referenced by configure_from_filter_tag().

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::sidechain_sidechain ( ) const

inline

Get whether we're counting sidechain-sidechain hbonds:

References sidechain_sidechain_.

Referenced by configure_from_filter_tag(), and count_hbonds().

Friends And Related Function Documentation

friend class ::PeptideInternalHbondsMetricTests

friend

Member Data Documentation

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_backbone_ = true

private

Are we counting backbone-backbone hydrogen bonds? Default true.

Referenced by backbone_backbone(), count_hbonds(), and set_hbond_types().

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::backbone_sidechain_ = false

private

Are we counting backbone-sidechain hydrogen bonds? Default false.

Referenced by backbone_sidechain(), count_hbonds(), and set_hbond_types().

core::Size protocols::cyclic_peptide::PeptideInternalHbondsMetric::exclusion_distance_ = 1

private

The number of residues apart in terms of covalent connectivity that two residues have to be in order for their hydrogen bonds to be counted. Defaults to 1.

Referenced by exclusion_distance(), and set_exclusion_distance().

core::Real protocols::cyclic_peptide::PeptideInternalHbondsMetric::hbond_energy_cutoff_ = -0.25

private

The energy cutoff for counting a hydrogen bond. Defaults to -0.25.

Referenced by hbond_energy_cutoff(), and set_hbond_energy_cutoff().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::PeptideInternalHbondsMetric::residue_selector_

private

The residue selector. If none is provided, we evaluate the whole pose.

Referenced by calculate(), provide_citation_info(), report(), residue_selector(), and set_residue_selector().

core::scoring::ScoreFunctionCOP protocols::cyclic_peptide::PeptideInternalHbondsMetric::scorefxn_

mutableprivate

The scorefunction to use for evaluating hydrogen bonds. If none is provided, we'll grab the default scorefunction and cache it.

Referenced by count_hbonds(), provide_citation_info(), scorefxn(), and set_scorefxn().

bool protocols::cyclic_peptide::PeptideInternalHbondsMetric::sidechain_sidechain_ = false

private

Are we counting sidechain-sidechain hydrogen bonds? Default false.

Referenced by count_hbonds(), set_hbond_types(), and sidechain_sidechain().

The documentation for this class was generated from the following files:

src/protocols/cyclic_peptide/PeptideInternalHbondsMetric.hh
src/protocols/cyclic_peptide/PeptideInternalHbondsMetric.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation