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protocols::fldsgn::filters::HSSTripletFilter Class Reference

#include <HSSTripletFilter.hh>

Inheritance diagram for protocols::fldsgn::filters::HSSTripletFilter:
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::SS_Info2 
SS_Info2
 
typedef
protocols::fldsgn::topology::HSSTriplet 
HSSTriplet
 
typedef
protocols::fldsgn::topology::HSSTriplets 
HSSTriplets
 
typedef
protocols::fldsgn::topology::HSSTripletSet 
HSSTripletSet
 
typedef
protocols::fldsgn::topology::HSSTripletSetOP 
HSSTripletSetOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 HSSTripletFilter ()
 default constructor More...
 
 HSSTripletFilter (HSSTriplets const &hss3s)
 constructor with arguments More...
 
 HSSTripletFilter (String const &hss3s)
 constructor with arguments More...
 
 HSSTripletFilter (HSSTripletFilter const &rval)
 copy constructor – required because we clone the hss3set_ pointer More...
 
 ~HSSTripletFilter () override
 
FilterOP clone () const override
 
FilterOP fresh_instance () const override
 
void add_hsstriplets (String const &hss3s)
 add filtered HSSTriplets from string More...
 
void add_hsstriplets (HSSTriplets const &hss3s)
 
void secstruct (String const &ss)
 
void filter_min_dist (Real const r)
 
void filter_max_dist (Real const r)
 maximum distance for filtering More...
 
void filter_min_angle (Real const r)
 miniimum angle for filtering More...
 
void filter_max_angle (Real const r)
 maximum angle for filtering More...
 
void output_id (core::Size const i)
 set output id More...
 
void output_type (String const &s)
 set output type 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

String get_secstruct (Pose const &pose) const
 computes and returns secondary structure string to use for this filter. More...
 
HSSTriplets get_hss3s (Pose const &pose) const
 returns HSSTriplets object to use for this filter More...
 
bool check_elements (HSSTriplet const &hss, SS_Info2 const &ss_info) const
 checks secondary structure elements in the triplet, returns false if invalid More...
 
Real compute_dist (HSSTriplet const &hss) const
 given an HSS triplet, compute the distance from helix to sheet More...
 
Real compute_angle (Real const angle) const
 given an hs-angle, return a valid angle accounting for ignore_helix_direction_ if ignore_helix_direction_ is true, this basically makes angle periodic from -90 to 90 More...
 

Private Attributes

HSSTripletSetOP hss3set_
 hsstriplet More...
 
String secstruct_
 if value is empty, dssp will run for ss definition ( default is emptry ) More...
 
Real filter_min_dist_
 filtered min distance between helix and sheet More...
 
Real filter_max_dist_
 filtered max distance between helix and sheet More...
 
Real filter_min_angle_
 filtered min angle between helix and sheet More...
 
Real filter_max_angle_
 filtered max angle between helix and sheet More...
 
core::Size output_id_
 output id of HSSTriplet More...
 
String output_type_
 output type, dist or angle More...
 
bool ignore_helix_direction_
 if set, the filter will ignore the direction of the helix and return an angle between -90 and 90 instead of -180 and 180 More...
 
bool use_dssp_
 if set, and secstruct_ is empty, secondary structure will be determined by dssp. Otherwise, it will be taken from the pose. More...
 

Additional Inherited Members

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

Member Typedef Documentation

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

Constructor & Destructor Documentation

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( )

default constructor

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( HSSTriplets const &  hss3s)

constructor with arguments

protocols::fldsgn::filters::HSSTripletFilter::HSSTripletFilter ( String const &  hss3s)

constructor with arguments

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

copy constructor – required because we clone the hss3set_ pointer

References hss3set_.

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

Member Function Documentation

void protocols::fldsgn::filters::HSSTripletFilter::add_hsstriplets ( String const &  hss3s)

add filtered HSSTriplets from string

set filtered HSSTriplets from string

References protocols::fldsgn::topology::HSSTripletSet::hss_triplets().

Referenced by parse_my_tag().

void protocols::fldsgn::filters::HSSTripletFilter::add_hsstriplets ( HSSTriplets const &  hss3s)

References hss3set_.

bool protocols::fldsgn::filters::HSSTripletFilter::apply ( Pose const &  pose) const
overridevirtual
bool protocols::fldsgn::filters::HSSTripletFilter::check_elements ( topology::HSSTriplet const &  hss,
topology::SS_Info2 const &  ss_info 
) const
private

checks secondary structure elements in the triplet, returns false if invalid

If the pose doesn't contain the helix or strands, returns false If the length of the helix is < 5, returns false If the length of either strand is < 2, returns false

References protocols::fldsgn::topology::SS_Info2::helices(), protocols::fldsgn::topology::HSSTriplet::helix(), protocols::fldsgn::topology::HSSTriplet::strand1(), protocols::fldsgn::topology::HSSTriplet::strand2(), protocols::fldsgn::topology::SS_Info2::strands(), and protocols::fldsgn::TR().

Referenced by apply(), and compute().

std::string protocols::fldsgn::filters::HSSTripletFilter::class_name ( )
static
FilterOP protocols::fldsgn::filters::HSSTripletFilter::clone ( ) const
inlineoverridevirtual
HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute ( Pose const &  pose) const
HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute_angle ( core::Real const  angle) const
private

given an hs-angle, return a valid angle accounting for ignore_helix_direction_ if ignore_helix_direction_ is true, this basically makes angle periodic from -90 to 90

References ignore_helix_direction_.

Referenced by apply(), and compute().

HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::compute_dist ( HSSTriplet const &  hss) const
private

given an HSS triplet, compute the distance from helix to sheet

References protocols::fldsgn::topology::HSSTriplet::hs1_dist(), and protocols::fldsgn::topology::HSSTriplet::hs2_dist().

Referenced by apply().

void protocols::fldsgn::filters::HSSTripletFilter::filter_max_angle ( Real const  r)

maximum angle for filtering

References filter_max_angle_.

void protocols::fldsgn::filters::HSSTripletFilter::filter_max_dist ( Real const  r)

maximum distance for filtering

References filter_max_dist_.

void protocols::fldsgn::filters::HSSTripletFilter::filter_min_angle ( Real const  r)

miniimum angle for filtering

References filter_min_angle_.

void protocols::fldsgn::filters::HSSTripletFilter::filter_min_dist ( Real const  r)

References filter_min_dist_.

FilterOP protocols::fldsgn::filters::HSSTripletFilter::fresh_instance ( ) const
inlineoverridevirtual
HSSTripletFilter::HSSTriplets protocols::fldsgn::filters::HSSTripletFilter::get_hss3s ( Pose const &  pose) const
private

returns HSSTriplets object to use for this filter

if hss triplets are given prior to apply time, returns those otherwise, look for HSS info in the pose's StructureData and return that

References protocols::denovo_design::components::StructureDataFactory::get_from_const_pose(), hss3set_, protocols::fldsgn::topology::HSSTripletSet::hss_triplets(), and protocols::fldsgn::TR().

Referenced by apply(), and compute().

HSSTripletFilter::String protocols::fldsgn::filters::HSSTripletFilter::get_secstruct ( Pose const &  pose) const
private

computes and returns secondary structure string to use for this filter.

if secstruct_ is non-empty, returns that if use_dssp_ is true, use DSSP to compute secstruct otherwise, use secstruct stored in the pose

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

Referenced by apply(), and compute().

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

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::HSSTripletFilter::output_id ( core::Size const  i)

set output id

maximum angle for filtering

References output_id_.

void protocols::fldsgn::filters::HSSTripletFilter::output_type ( String const &  s)

set output type

References output_type_.

void protocols::fldsgn::filters::HSSTripletFilter::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::fldsgn::filters::HSSTripletFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
HSSTripletFilter::Real protocols::fldsgn::filters::HSSTripletFilter::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::HSSTripletFilter::secstruct ( String const &  ss)

References secstruct_.

Referenced by apply(), and compute().

Member Data Documentation

Real protocols::fldsgn::filters::HSSTripletFilter::filter_max_angle_
private

filtered max angle between helix and sheet

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

Real protocols::fldsgn::filters::HSSTripletFilter::filter_max_dist_
private

filtered max distance between helix and sheet

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

Real protocols::fldsgn::filters::HSSTripletFilter::filter_min_angle_
private

filtered min angle between helix and sheet

Referenced by filter_min_angle(), and parse_my_tag().

Real protocols::fldsgn::filters::HSSTripletFilter::filter_min_dist_
private

filtered min distance between helix and sheet

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

HSSTripletSetOP protocols::fldsgn::filters::HSSTripletFilter::hss3set_
private
bool protocols::fldsgn::filters::HSSTripletFilter::ignore_helix_direction_
private

if set, the filter will ignore the direction of the helix and return an angle between -90 and 90 instead of -180 and 180

Referenced by compute_angle(), and parse_my_tag().

core::Size protocols::fldsgn::filters::HSSTripletFilter::output_id_
private

output id of HSSTriplet

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

String protocols::fldsgn::filters::HSSTripletFilter::output_type_
private

output type, dist or angle

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

String protocols::fldsgn::filters::HSSTripletFilter::secstruct_
private

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

Referenced by get_secstruct(), parse_my_tag(), and secstruct().

bool protocols::fldsgn::filters::HSSTripletFilter::use_dssp_
private

if set, and secstruct_ is empty, secondary structure will be determined by dssp. Otherwise, it will be taken from the pose.

Referenced by get_secstruct(), and parse_my_tag().


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