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

#include <HelixPairingFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HelixPairingFilter:
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Collaboration diagram for protocols::fldsgn::filters::HelixPairingFilter:
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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::TagPtr TagPtr
 
typedef
protocols::filters::Filters_map 		Filters_map
 
typedef protocols::moves::DataMap DataMap
 
typedef
protocols::moves::Movers_map 		Movers_map
 

Public Member Functions

 HelixPairingFilter ()
 
 HelixPairingFilter (String const &hf)
 
 HelixPairingFilter (HelixPairings const &hpairs)
 
 HelixPairingFilter (HelixPairingFilter const &rval)
 
virtual ~HelixPairingFilter ()
 
virtual FilterOP clone () const
 
virtual FilterOP fresh_instance () const
 
void helix_pairings (String const &hpairs)
 
void helix_pairings (HelixPairings const &hpairs)
 
void secstruct (String const &ss)
 
virtual std::string name () const
 
virtual void parse_my_tag (TagPtr const tag, DataMap &, Filters_map const &, Movers_map const &, Pose const &)
 parse xml More...
 
Real report_sm (Pose const &pose) const
 used to report filter internals through a score or silent file More...
 
Real compute (Pose const &pose) const
 
virtual bool apply (Pose const &pose) const
 Returns true if the given pose passes the filter, false otherwise. More...
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
virtual ~Filter ()
 
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 void apply (core::io::serialization::PipeMap &pmap)
 
virtual void score (core::io::serialization::PipeMap &pmap)
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 

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...
 
Size output_id_
 HelixPairing id for output. More...
 
String output_type_
 output type, dist or angle More...
 

Additional Inherited Members

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

Detailed Description

Definition at line 46 of file HelixPairingFilter.hh.

Member Typedef Documentation

typedef protocols::moves::DataMap protocols::fldsgn::filters::HelixPairingFilter::DataMap

Definition at line 64 of file HelixPairingFilter.hh.

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixPairingFilter::Filter

Definition at line 51 of file HelixPairingFilter.hh.

typedef protocols::filters::FilterOP protocols::fldsgn::filters::HelixPairingFilter::FilterOP

Definition at line 55 of file HelixPairingFilter.hh.

typedef protocols::filters::Filters_map protocols::fldsgn::filters::HelixPairingFilter::Filters_map

Definition at line 63 of file HelixPairingFilter.hh.

typedef protocols::fldsgn::topology::HelixPairing protocols::fldsgn::filters::HelixPairingFilter::HelixPairing

Definition at line 57 of file HelixPairingFilter.hh.

typedef protocols::fldsgn::topology::HelixPairings protocols::fldsgn::filters::HelixPairingFilter::HelixPairings

Definition at line 58 of file HelixPairingFilter.hh.

typedef protocols::fldsgn::topology::HelixPairingSet protocols::fldsgn::filters::HelixPairingFilter::HelixPairingSet

Definition at line 59 of file HelixPairingFilter.hh.

typedef protocols::fldsgn::topology::HelixPairingSetOP protocols::fldsgn::filters::HelixPairingFilter::HelixPairingSetOP

Definition at line 60 of file HelixPairingFilter.hh.

typedef protocols::moves::Movers_map protocols::fldsgn::filters::HelixPairingFilter::Movers_map

Definition at line 65 of file HelixPairingFilter.hh.

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

Definition at line 56 of file HelixPairingFilter.hh.

typedef core::Real protocols::fldsgn::filters::HelixPairingFilter::Real

Definition at line 53 of file HelixPairingFilter.hh.

typedef core::Size protocols::fldsgn::filters::HelixPairingFilter::Size

Definition at line 54 of file HelixPairingFilter.hh.

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

Definition at line 52 of file HelixPairingFilter.hh.

typedef protocols::filters::Filter protocols::fldsgn::filters::HelixPairingFilter::Super

Definition at line 50 of file HelixPairingFilter.hh.

typedef utility::tag::TagPtr protocols::fldsgn::filters::HelixPairingFilter::TagPtr

Definition at line 62 of file HelixPairingFilter.hh.

Constructor & Destructor Documentation

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( )

Definition at line 51 of file HelixPairingFilter.cc.

Referenced by clone(), and fresh_instance().

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( String const &  hf)

Definition at line 72 of file HelixPairingFilter.cc.

References hpairset_.

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

Definition at line 61 of file HelixPairingFilter.cc.

protocols::fldsgn::filters::HelixPairingFilter::HelixPairingFilter ( HelixPairingFilter const &  rval)

Definition at line 84 of file HelixPairingFilter.cc.

virtual protocols::fldsgn::filters::HelixPairingFilter::~HelixPairingFilter ( )
inlinevirtual

Definition at line 83 of file HelixPairingFilter.hh.

Member Function Documentation

bool protocols::fldsgn::filters::HelixPairingFilter::apply ( Pose const &  pose) const
virtual

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

Implements protocols::filters::Filter.

Definition at line 122 of file HelixPairingFilter.cc.

References protocols::fldsgn::topology::HelixPairing::align_angle(), align_angle_, bend_angle_, protocols::fldsgn::topology::HelixPairingSet::calc_geometry(), protocols::fldsgn::topology::HelixPairing::cross_angle(), cross_angle_, protocols::fldsgn::topology::HelixPairing::dist(), dist_cutoff_, protocols::fldsgn::topology::HelixPairing::h1(), protocols::fldsgn::topology::HelixPairing::h2(), helix_pairings(), protocols::fldsgn::topology::HelixPairingSet::helix_pairings(), hpairset_, secstruct_, core::pose::Pose::total_residue(), and protocols::fldsgn::TR().

virtual FilterOP protocols::fldsgn::filters::HelixPairingFilter::clone ( ) const
inlinevirtual

Implements protocols::filters::Filter.

Definition at line 90 of file HelixPairingFilter.hh.

References HelixPairingFilter().

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

Definition at line 209 of file HelixPairingFilter.cc.

References protocols::fldsgn::topology::HelixPairingSet::calc_geometry(), protocols::fldsgn::topology::HelixPairingSet::helix_pairing(), helix_pairings(), protocols::fldsgn::topology::HelixPairingSet::helix_pairings(), hpairset_, output_id_, output_type_, secstruct_, core::pose::Pose::total_residue(), and protocols::fldsgn::TR().

Referenced by report_sm().

virtual FilterOP protocols::fldsgn::filters::HelixPairingFilter::fresh_instance ( ) const
inlinevirtual

Implements protocols::filters::Filter.

Definition at line 93 of file HelixPairingFilter.hh.

References HelixPairingFilter().

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

Definition at line 102 of file HelixPairingFilter.cc.

References hpairset_.

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

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

Definition at line 96 of file HelixPairingFilter.cc.

References hpairset_.

virtual std::string protocols::fldsgn::filters::HelixPairingFilter::name ( ) const
inlinevirtual

Reimplemented from protocols::filters::Filter.

Definition at line 110 of file HelixPairingFilter.hh.

void protocols::fldsgn::filters::HelixPairingFilter::parse_my_tag ( TagPtr const  tag,
DataMap &  ,
Filters_map const &  ,
Movers_map const &  ,
Pose const &   
)
virtual

parse xml

Reimplemented from protocols::filters::Filter.

Definition at line 256 of file HelixPairingFilter.cc.

References align_angle_, bend_angle_, cross_angle_, dist_cutoff_, helix_pairings(), hpairset_, output_id_, output_type_, secstruct_, and protocols::fldsgn::TR().

HelixPairingFilter::Real protocols::fldsgn::filters::HelixPairingFilter::report_sm ( Pose const &  ) const
virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 115 of file HelixPairingFilter.cc.

References compute().

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

Definition at line 108 of file HelixPairingFilter.cc.

References secstruct_.

Member Data Documentation

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

Definition at line 155 of file HelixPairingFilter.hh.

Referenced by apply(), and parse_my_tag().

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

Definition at line 149 of file HelixPairingFilter.hh.

Referenced by apply(), and parse_my_tag().

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

Definition at line 152 of file HelixPairingFilter.hh.

Referenced by apply(), and parse_my_tag().

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

Definition at line 146 of file HelixPairingFilter.hh.

Referenced by apply(), and parse_my_tag().

HelixPairingSetOP protocols::fldsgn::filters::HelixPairingFilter::hpairset_
private

helix pairings

Definition at line 158 of file HelixPairingFilter.hh.

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

Size protocols::fldsgn::filters::HelixPairingFilter::output_id_
private

HelixPairing id for output.

Definition at line 161 of file HelixPairingFilter.hh.

Referenced by compute(), and parse_my_tag().

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

output type, dist or angle

Definition at line 164 of file HelixPairingFilter.hh.

Referenced by compute(), and parse_my_tag().

String protocols::fldsgn::filters::HelixPairingFilter::secstruct_
mutableprivate

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

Definition at line 143 of file HelixPairingFilter.hh.

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

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