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protocols::fldsgn::filters::HelixPairingFilter Class Reference

#include <HelixPairingFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HelixPairingFilter:
Inheritance graph
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Public Types

typedef protocols::filters::Filter Super
 
typedef protocols::filters::Filter Filter
 
typedef std::string String
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef core::pose::Pose Pose
 
typedef
protocols::fldsgn::topology::HelixPairing 
HelixPairing
 
typedef
protocols::fldsgn::topology::HelixPairings 
HelixPairings
 
typedef
protocols::fldsgn::topology::HelixPairingSet 
HelixPairingSet
 
typedef
protocols::fldsgn::topology::HelixPairingSetOP 
HelixPairingSetOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 HelixPairingFilter ()
 
 HelixPairingFilter (String const &hf)
 
 HelixPairingFilter (HelixPairings const &hpairs)
 
 HelixPairingFilter (HelixPairingFilter const &rval)
 
 ~HelixPairingFilter () override
 
FilterOP clone () const override
 
FilterOP fresh_instance () const override
 
void helix_pairings (String const &hpairs)
 
void helix_pairings (HelixPairings const &hpairs)
 
void secstruct (String const &ss)
 
void dist (Real const dist_val)
 sets distance cutoff More...
 
void bend_angle (Real const bend_angle_val)
 sets max helix bend More...
 
void cross_angle (Real const cross_angle_val)
 sets max cross angle More...
 
void align_angle (Real const align_angle_val)
 sets max alignment angle More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
Real report_sm (Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
Real compute (Pose const &pose) const
 
bool apply (Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual void report (std::ostream &, core::pose::Pose const &) const
 
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 bool filter_provides_citation_info () const
 Does this filter provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool filter_is_unpublished () const
 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

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

Private Member Functions

std::string secstruct (core::pose::Pose const &pose) const
 returns secondary structure to be used for finding helices More...
 
topology::HelixPairingSet compute_helix_pairing_set (core::pose::Pose const &pose) const
 Returns the Helix pairing set to filter based on. More...
 
std::set< core::Sizefind_missing_helices (topology::SS_Info2 const &ss_info, topology::HelixPairings const &hpairs) const
 Returns set of helix IDs that were not found in the pose. Set is empty if all helices are present. More...
 

Private Attributes

String secstruct_
 if value is empty, dssp will run for ss definition ( default is emptry ) More...
 
Real dist_cutoff_
 
Real bend_angle_
 
Real cross_angle_
 
Real align_angle_
 
HelixPairingSetOP hpairset_
 helix pairings More...
 
core::Size output_id_
 HelixPairing id for output. More...
 
String output_type_
 output type, dist or angle More...
 
bool use_dssp_
 if true, and secstruct_ is empty, DSSP will be used to determine secondary structure of the pose More...
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( )
protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( String const &  hf)
protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( HelixPairings const &  hpairs)
protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( HelixPairingFilter const &  rval)

References hpairset_.

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

Member Function Documentation

void protocols::fldsgn::filters::HelixPairingFilter::align_angle ( Real const  align_angle_val)

sets max alignment angle

References align_angle_.

bool protocols::fldsgn::filters::HelixPairingFilter::apply ( Pose const &  pose) const
overridevirtual
void protocols::fldsgn::filters::HelixPairingFilter::bend_angle ( Real const  bend_angle_val)

sets max helix bend

References bend_angle_.

std::string protocols::fldsgn::filters::HelixPairingFilter::class_name ( )
static
FilterOP protocols::fldsgn::filters::HelixPairingFilter::clone ( ) const
inlineoverridevirtual
HelixPairingFilter::Real protocols::fldsgn::filters::HelixPairingFilter::compute ( Pose const &  pose) const
topology::HelixPairingSet protocols::fldsgn::filters::HelixPairingFilter::compute_helix_pairing_set ( core::pose::Pose const &  pose) const
private

Returns the Helix pairing set to filter based on.

If hpairset_ is set, returns that. Otherwise, look up the pairing set using the StructureData cached in the pose

References hpairset_, and protocols::fldsgn::TR().

Referenced by apply(), and compute().

void protocols::fldsgn::filters::HelixPairingFilter::cross_angle ( Real const  cross_angle_val)

sets max cross angle

References cross_angle_.

void protocols::fldsgn::filters::HelixPairingFilter::dist ( Real const  dist_val)

sets distance cutoff

References dist_cutoff_.

std::set< core::Size > protocols::fldsgn::filters::HelixPairingFilter::find_missing_helices ( topology::SS_Info2 const &  ss_info,
topology::HelixPairings const &  hpairs 
) const
private

Returns set of helix IDs that were not found in the pose. Set is empty if all helices are present.

References protocols::antibody::h1, protocols::antibody::h2, and protocols::fldsgn::topology::SS_Info2::helices().

Referenced by apply(), and compute().

FilterOP protocols::fldsgn::filters::HelixPairingFilter::fresh_instance ( ) const
inlineoverridevirtual
void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings ( String const &  hpairs)

References hpairset_.

Referenced by apply(), compute(), and parse_my_tag().

void protocols::fldsgn::filters::HelixPairingFilter::helix_pairings ( HelixPairings const &  hpairs)

References hpairset_.

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

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::HelixPairingFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::fldsgn::filters::HelixPairingFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
HelixPairingFilter::Real protocols::fldsgn::filters::HelixPairingFilter::report_sm ( Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::fldsgn::filters::HelixPairingFilter::secstruct ( String const &  ss)

References secstruct_.

Referenced by apply(), and compute().

std::string protocols::fldsgn::filters::HelixPairingFilter::secstruct ( core::pose::Pose const &  pose) const
private

returns secondary structure to be used for finding helices

If secstruct_ is set, returns that. If use_dssp_ is true, returns secstruct from DSSP Otherwise, returns the pose.secstruct()

References protocols::simple_filters::dssp(), core::pose::Pose::secstruct(), secstruct_, and use_dssp_.

Member Data Documentation

Real protocols::fldsgn::filters::HelixPairingFilter::align_angle_
private

Referenced by align_angle(), apply(), and parse_my_tag().

Real protocols::fldsgn::filters::HelixPairingFilter::bend_angle_
private

Referenced by apply(), bend_angle(), and parse_my_tag().

Real protocols::fldsgn::filters::HelixPairingFilter::cross_angle_
private

Referenced by apply(), cross_angle(), and parse_my_tag().

Real protocols::fldsgn::filters::HelixPairingFilter::dist_cutoff_
private

Referenced by apply(), dist(), and parse_my_tag().

HelixPairingSetOP protocols::fldsgn::filters::HelixPairingFilter::hpairset_
private
core::Size protocols::fldsgn::filters::HelixPairingFilter::output_id_
private

HelixPairing id for output.

Referenced by compute(), and parse_my_tag().

String protocols::fldsgn::filters::HelixPairingFilter::output_type_
private

output type, dist or angle

Referenced by compute(), and parse_my_tag().

String protocols::fldsgn::filters::HelixPairingFilter::secstruct_
private

if value is empty, dssp will run for ss definition ( default is emptry )

Referenced by parse_my_tag(), and secstruct().

bool protocols::fldsgn::filters::HelixPairingFilter::use_dssp_
private

if true, and secstruct_ is empty, DSSP will be used to determine secondary structure of the pose

Referenced by parse_my_tag(), and secstruct().


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