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Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::fldsgn::filters::InterlockingAromaFilter Class Reference

#include <InterlockingAromaFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::InterlockingAromaFilter:
Inheritance graph
[legend]

Public Types

typedef protocols::filters::Filter Super
 
typedef protocols::filters::Filter Filter
 
typedef protocols::filters::FilterOP FilterOP
 
typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef std::string String
 
typedef protocols::fldsgn::topology::SS_Info2_COP SS_Info2_COP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 InterlockingAromaFilter ()
 
 InterlockingAromaFilter (String const &type)
 
 InterlockingAromaFilter (InterlockingAromaFilter const &rval)
 
 ~InterlockingAromaFilter () override
 
FilterOP clone () const override
 
FilterOP fresh_instance () const override
 
void filter_value (Real const value)
 
void contact_distance (Real const value)
 
void verbose (bool const b)
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
bool apply (Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
Real report_sm (Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
void report (std::ostream &out, Pose const &pose) const override
 used to report score More...
 
Real compute (Pose const &pose) const
 compute this filter More...
 
bool compute (core::Size const &res, Pose const &pose, SS_Info2_COP const ssinfo) const
 compute this filter for a give residue More...
 
std::string name () const override
 
- 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)
 
virtual void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Static Public Member Functions

static std::string class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Attributes

Real filter_value_
 
Real contact_dist2_
 
String input_ss_
 
bool verbose_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::fldsgn::filters::InterlockingAromaFilter::DataMap

◆ Filter

typedef protocols::filters::Filter protocols::fldsgn::filters::InterlockingAromaFilter::Filter

◆ FilterOP

typedef protocols::filters::FilterOP protocols::fldsgn::filters::InterlockingAromaFilter::FilterOP

◆ Pose

typedef core::pose::Pose protocols::fldsgn::filters::InterlockingAromaFilter::Pose

◆ Real

typedef core::Real protocols::fldsgn::filters::InterlockingAromaFilter::Real

◆ SS_Info2_COP

typedef protocols::fldsgn::topology::SS_Info2_COP protocols::fldsgn::filters::InterlockingAromaFilter::SS_Info2_COP

◆ String

typedef std::string protocols::fldsgn::filters::InterlockingAromaFilter::String

◆ Super

typedef protocols::filters::Filter protocols::fldsgn::filters::InterlockingAromaFilter::Super

◆ TagCOP

typedef utility::tag::TagCOP protocols::fldsgn::filters::InterlockingAromaFilter::TagCOP

Constructor & Destructor Documentation

◆ InterlockingAromaFilter() [1/3]

protocols::fldsgn::filters::InterlockingAromaFilter::InterlockingAromaFilter ( )

◆ InterlockingAromaFilter() [2/3]

protocols::fldsgn::filters::InterlockingAromaFilter::InterlockingAromaFilter ( String const &  type)

◆ InterlockingAromaFilter() [3/3]

protocols::fldsgn::filters::InterlockingAromaFilter::InterlockingAromaFilter ( InterlockingAromaFilter const &  rval)
default

◆ ~InterlockingAromaFilter()

protocols::fldsgn::filters::InterlockingAromaFilter::~InterlockingAromaFilter ( )
inlineoverride

Member Function Documentation

◆ apply()

bool protocols::fldsgn::filters::InterlockingAromaFilter::apply ( Pose const &  pose) const
overridevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

References compute(), filter_value_, and tr().

◆ class_name()

std::string protocols::fldsgn::filters::InterlockingAromaFilter::class_name ( )
static

Referenced by protocols::fldsgn::filters::InterlockingAromaFilterCreator::keyname(), name(), and provide_xml_schema().

◆ clone()

FilterOP protocols::fldsgn::filters::InterlockingAromaFilter::clone ( ) const
inlineoverridevirtual

Implements protocols::filters::Filter.

◆ compute() [1/2]

bool protocols::fldsgn::filters::InterlockingAromaFilter::compute ( core::Size const &  res,
Pose const &  pose,
SS_Info2_COP const  ssinfo 
) const

compute this filter for a give residue

References core::pose::Pose::aa(), core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, core::conformation::Residue::atom(), core::conformation::Residue::atom_type(), core::chemical::AtomType::atom_type_name(), contact_dist2_, core::pose::Pose::energies(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), tr(), and core::conformation::Atom::xyz().

◆ compute() [2/2]

InterlockingAromaFilter::Real protocols::fldsgn::filters::InterlockingAromaFilter::compute ( Pose const &  pose) const

compute this filter

References core::pose::Pose::aa(), core::chemical::aa_phe, core::chemical::aa_trp, core::chemical::aa_tyr, protocols::simple_filters::dssp(), input_ss_, and core::pose::Pose::size().

Referenced by apply(), report(), and report_sm().

◆ contact_distance()

void protocols::fldsgn::filters::InterlockingAromaFilter::contact_distance ( Real const  value)

References contact_dist2_, and core::scoring::electron_density::square().

Referenced by parse_my_tag().

◆ filter_value()

void protocols::fldsgn::filters::InterlockingAromaFilter::filter_value ( Real const  value)

References filter_value_.

Referenced by parse_my_tag().

◆ fresh_instance()

FilterOP protocols::fldsgn::filters::InterlockingAromaFilter::fresh_instance ( ) const
inlineoverridevirtual

Implements protocols::filters::Filter.

◆ name()

std::string protocols::fldsgn::filters::InterlockingAromaFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

◆ parse_my_tag()

void protocols::fldsgn::filters::InterlockingAromaFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

parse xml

Reimplemented from protocols::filters::Filter.

References contact_distance(), filter_value(), input_ss_, protocols::parser::BluePrint::secstruct(), and verbose_.

◆ provide_xml_schema()

void protocols::fldsgn::filters::InterlockingAromaFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::fldsgn::filters::InterlockingAromaFilterCreator::provide_xml_schema().

◆ report()

void protocols::fldsgn::filters::InterlockingAromaFilter::report ( std::ostream &  out,
Pose const &  pose 
) const
overridevirtual

used to report score

Reimplemented from protocols::filters::Filter.

References compute(), and core::conformation::membrane::out.

◆ report_sm()

InterlockingAromaFilter::Real protocols::fldsgn::filters::InterlockingAromaFilter::report_sm ( Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

◆ verbose()

void protocols::fldsgn::filters::InterlockingAromaFilter::verbose ( bool const  b)

References protocols::match::upstream::b, and verbose_.

Member Data Documentation

◆ contact_dist2_

Real protocols::fldsgn::filters::InterlockingAromaFilter::contact_dist2_
private

Referenced by compute(), and contact_distance().

◆ filter_value_

Real protocols::fldsgn::filters::InterlockingAromaFilter::filter_value_
private

Referenced by apply(), and filter_value().

◆ input_ss_

String protocols::fldsgn::filters::InterlockingAromaFilter::input_ss_
private

Referenced by compute(), and parse_my_tag().

◆ verbose_

bool protocols::fldsgn::filters::InterlockingAromaFilter::verbose_
private

Referenced by parse_my_tag(), and verbose().

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