A filter that thinly wraps the PeptideInternalHbondsMetric. More...

#include <PeptideInternalHbondsFilter.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideInternalHbondsFilter:

Public Member Functions
	PeptideInternalHbondsFilter ()
	Default constructor. More...

	~PeptideInternalHbondsFilter () override=default
	Default destructor. More...

protocols::filters::FilterOP	fresh_instance () const override
	Required in the context of the parser/scripting scheme. More...

protocols::filters::FilterOP	clone () const override
	Make a copy of this filter and return an owning pointer to the copy. More...

bool	apply (core::pose::Pose const &pose) const override
	returns true if the structure has internal hbonds equal to or greater than the cutoff, false otherwise. More...

core::Real	report_sm (core::pose::Pose const &pose) const override
	Required for reporting score values. More...

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

std::string	name () const override

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parse XML tag (to use this Filter in Rosetta Scripts). 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...

void	set_hbond_cutoff (core::Size const setting)
	Set the threshold number of internal hydrogen bonds, below which the filter fails. 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...

core::Size	hbond_cutoff () const
	Get the threshold number of internal hydrogen bonds, below which the filter fails. More...

PeptideInternalHbondsMetric const &	hbond_metric () const
	Access the internal PeptideInternalHbondsMetric used by this filter (const access). More...

PeptideInternalHbondsMetric &	hbond_metric ()
	Access the internal PeptideInternalHbondsMetric used by this filter (non-const access). More...

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

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	~Filter () override

virtual std::string	get_type () const

std::string	get_user_defined_name () const

void	set_user_defined_name (std::string const &name)

virtual void	clear ()
	used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...

virtual core::Real	score (core::pose::Pose &pose)

Static Public Member Functions
static std::string	class_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
	Describe the XML interface in a machine-readable way. More...

Private Attributes
PeptideInternalHbondsMetricOP	hbond_metric_
	The simple metric that we wrap. More...

core::Size	hbond_cutoff_ = 1
	The threshold number of internal hydrogen bonds, below which the filter fails. More...

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Detailed Description

A filter that thinly wraps the PeptideInternalHbondsMetric.

Constructor & Destructor Documentation

◆ PeptideInternalHbondsFilter()

protocols::cyclic_peptide::PeptideInternalHbondsFilter::PeptideInternalHbondsFilter ( )

Default constructor.

◆ ~PeptideInternalHbondsFilter()

protocols::cyclic_peptide::PeptideInternalHbondsFilter::~PeptideInternalHbondsFilter ( )

overridedefault

Default destructor.

Member Function Documentation

◆ apply()

bool protocols::cyclic_peptide::PeptideInternalHbondsFilter::apply ( core::pose::Pose const & pose ) const

overridevirtual

returns true if the structure has internal hbonds equal to or greater than the cutoff, false otherwise.

Implements protocols::filters::Filter.

References hbond_cutoff_, hbond_metric_, and protocols::cyclic_peptide::TR().

◆ backbone_backbone()

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

Get whether we're counting backbone-backbone hbonds:

References hbond_metric_.

◆ backbone_sidechain()

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

Get whether we're counting backbone-sidechain hbonds:

References hbond_metric_.

◆ class_name()

std::string protocols::cyclic_peptide::PeptideInternalHbondsFilter::class_name ( )

static

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

◆ clone()

protocols::filters::FilterOP protocols::cyclic_peptide::PeptideInternalHbondsFilter::clone ( ) const

overridevirtual

Make a copy of this filter and return an owning pointer to the copy.

Implements protocols::filters::Filter.

◆ exclusion_distance()

core::Size protocols::cyclic_peptide::PeptideInternalHbondsFilter::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.

Defaults to 1.

References hbond_metric_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::cyclic_peptide::PeptideInternalHbondsFilter::fresh_instance ( ) const

overridevirtual

Required in the context of the parser/scripting scheme.

Implements protocols::filters::Filter.

◆ hbond_cutoff()

core::Size protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_cutoff ( ) const

inline

Get the threshold number of internal hydrogen bonds, below which the filter fails.

Defaults to 1.

References hbond_cutoff_.

Referenced by parse_my_tag().

◆ hbond_energy_cutoff()

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

Get the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

References hbond_metric_.

◆ hbond_metric() [1/2]

PeptideInternalHbondsMetric& protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_metric ( )

inline

Access the internal PeptideInternalHbondsMetric used by this filter (non-const access).

References hbond_metric_.

◆ hbond_metric() [2/2]

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

inline

Access the internal PeptideInternalHbondsMetric used by this filter (const access).

References hbond_metric_.

◆ name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

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

overridevirtual

Parse XML tag (to use this Filter in Rosetta Scripts).

Reimplemented from protocols::filters::Filter.

References hbond_cutoff(), hbond_metric_, and set_hbond_cutoff().

◆ provide_citation_info()

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

overridevirtual

Provide the citation.

Reimplemented from protocols::filters::Filter.

References class_name(), and hbond_metric_.

◆ provide_xml_schema()

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

static

Describe the XML interface in a machine-readable way.

References class_name(), protocols::cyclic_peptide::PeptideInternalHbondsMetric::provide_shared_xml_schema_elements(), and protocols::filters::xsd_type_definition_w_attributes().

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

◆ report()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::report	(	std::ostream &	os,
		core::pose::Pose const &	pose
	)		const

overridevirtual

allows printing data to a stream.

Reimplemented from protocols::filters::Filter.

References hbond_metric_.

◆ report_sm()

core::Real protocols::cyclic_peptide::PeptideInternalHbondsFilter::report_sm ( core::pose::Pose const & pose ) const

overridevirtual

Required for reporting score values.

Reimplemented from protocols::filters::Filter.

References hbond_metric_.

◆ residue_selector()

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

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

References hbond_metric_.

◆ scorefxn()

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

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

References hbond_metric_.

◆ set_exclusion_distance()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::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 hbond_metric_.

◆ set_hbond_cutoff()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::set_hbond_cutoff ( core::Size const setting )

inline

Set the threshold number of internal hydrogen bonds, below which the filter fails.

Defaults to 1.

References hbond_cutoff_.

Referenced by parse_my_tag().

◆ set_hbond_energy_cutoff()

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

Set the energy cutoff for counting a hydrogen bond.

Defaults to -0.25.

References hbond_metric_.

◆ set_hbond_types()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::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 hbond_metric_.

◆ set_residue_selector()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::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 hbond_metric_.

◆ set_scorefxn()

void protocols::cyclic_peptide::PeptideInternalHbondsFilter::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 hbond_metric_.

◆ sidechain_sidechain()

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

Get whether we're counting sidechain-sidechain hbonds:

References hbond_metric_.

Member Data Documentation

◆ hbond_cutoff_

core::Size protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_cutoff_ = 1

private

The threshold number of internal hydrogen bonds, below which the filter fails.

Defaults to 1.

Referenced by apply(), hbond_cutoff(), and set_hbond_cutoff().

◆ hbond_metric_

PeptideInternalHbondsMetricOP protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_metric_

private

The simple metric that we wrap.

Referenced by apply(), backbone_backbone(), backbone_sidechain(), exclusion_distance(), hbond_energy_cutoff(), hbond_metric(), parse_my_tag(), provide_citation_info(), report(), report_sm(), residue_selector(), scorefxn(), set_exclusion_distance(), set_hbond_energy_cutoff(), set_hbond_types(), set_residue_selector(), set_scorefxn(), and sidechain_sidechain().

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

src/protocols/cyclic_peptide/PeptideInternalHbondsFilter.hh
src/protocols/cyclic_peptide/PeptideInternalHbondsFilter.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PeptideInternalHbondsFilter()

◆ ~PeptideInternalHbondsFilter()

Member Function Documentation

◆ apply()

◆ backbone_backbone()

◆ backbone_sidechain()

◆ class_name()

◆ clone()

◆ exclusion_distance()

◆ fresh_instance()

◆ hbond_cutoff()

◆ hbond_energy_cutoff()

◆ hbond_metric() [1/2]

◆ hbond_metric() [2/2]

◆ name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ report()

◆ report_sm()

◆ residue_selector()

◆ scorefxn()

◆ set_exclusion_distance()

◆ set_hbond_cutoff()

◆ set_hbond_energy_cutoff()

◆ set_hbond_types()

◆ set_residue_selector()

◆ set_scorefxn()

◆ sidechain_sidechain()

Member Data Documentation

◆ hbond_cutoff_

◆ hbond_metric_