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protocols::cyclic_peptide::PeptideInternalHbondsFilter Class Reference

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

#include <PeptideInternalHbondsFilter.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideInternalHbondsFilter:
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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...
 
PeptideInternalHbondsMetrichbond_metric ()
 Access the internal PeptideInternalHbondsMetric used by this filter (non-const access). More...
 
bool filter_provides_citation_info () const override
 Does this filter provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
bool filter_is_unpublished () const override
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. More...
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter 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

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

Default constructor.

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

Default destructor.

Member Function Documentation

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().

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

Get whether we're counting backbone-backbone hbonds:

References hbond_metric_.

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

Get whether we're counting backbone-sidechain hbonds:

References hbond_metric_.

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

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_.

bool protocols::cyclic_peptide::PeptideInternalHbondsFilter::filter_is_unpublished ( ) const
overridevirtual

Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?

Returns
True, since this is unpublished.

Reimplemented from protocols::filters::Filter.

bool protocols::cyclic_peptide::PeptideInternalHbondsFilter::filter_provides_citation_info ( ) const
overridevirtual

Does this filter provide information about how to cite it?

Returns false.

Reimplemented from protocols::filters::Filter.

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

Required in the context of the parser/scripting scheme.

Implements protocols::filters::Filter.

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().

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_.

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

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

References hbond_metric_.

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

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

References hbond_metric_.

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

Reimplemented from protocols::filters::Filter.

References class_name().

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().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::cyclic_peptide::PeptideInternalHbondsFilter::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Also provides unpublished author information for residue selectors and scorefunctions used.

Reimplemented from protocols::filters::Filter.

References class_name(), and hbond_metric_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::cyclic_peptide::PeptideInternalHbondsFilter::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
An empty vector for this filter, since it's unpublished. Provides citations for the scorefunction and residue selector, if available, however.

Reimplemented from protocols::filters::Filter.

References hbond_metric_.

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

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_.

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_.

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_.

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_.

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().

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_.

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_.

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_.

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_.

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

Get whether we're counting sidechain-sidechain hbonds:

References hbond_metric_.

Member Data Documentation

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().

PeptideInternalHbondsMetricOP protocols::cyclic_peptide::PeptideInternalHbondsFilter::hbond_metric_
private

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