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protocols::fldsgn::filters::HelixBendFilter Class Reference

Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry. More...

#include <HelixBendFilter.hh>

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

Public Member Functions

 HelixBendFilter ()
 
 ~HelixBendFilter () override
 
void secstruct (std::string const &ss)
 set secondary structure More...
 
void set_secstruct_from_bp (std::string const &bp_file_path)
 set secondary structure using a blueprint file More...
 
void threshold (core::Real const r)
 minimum angle for filtering More...
 
void helix_id (core::Size const r)
 Strand id number. More...
 
bool apply (core::pose::Pose const &pose) const override
 returns true if the structure passes the filter, false otherwise More...
 
void compute (core::pose::Pose const &pose) const
 computes filter value 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...
 
protocols::filters::FilterOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::filters::FilterOP clone () const override
 required in the context of the parser/scripting scheme 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)
 
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 Attributes

std::string secstruct_
 
core::Real threshold_
 
core::Size helix_id_
 
bool filter_status_
 
core::Real filter_val_
 

Additional Inherited Members

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

Detailed Description

Filter used in 'Principles for designing proteins with cavities formed by curved b-sheets' to control helix geometry.

Constructor & Destructor Documentation

protocols::fldsgn::filters::HelixBendFilter::HelixBendFilter ( )
protocols::fldsgn::filters::HelixBendFilter::~HelixBendFilter ( )
overridedefault

Member Function Documentation

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

returns true if the structure passes the filter, false otherwise

Implements protocols::filters::Filter.

References compute(), filter_status_, secstruct_, core::pose::Pose::size(), and protocols::fldsgn::TR().

std::string protocols::fldsgn::filters::HelixBendFilter::class_name ( )
static
protocols::filters::FilterOP protocols::fldsgn::filters::HelixBendFilter::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

void protocols::fldsgn::filters::HelixBendFilter::compute ( core::pose::Pose const &  pose) const
protocols::filters::FilterOP protocols::fldsgn::filters::HelixBendFilter::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

void protocols::fldsgn::filters::HelixBendFilter::helix_id ( core::Size const  r)

Strand id number.

References helix_id_.

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

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::fldsgn::filters::HelixBendFilter::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 helix_id_, secstruct(), set_secstruct_from_bp(), and threshold_.

void protocols::fldsgn::filters::HelixBendFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::fldsgn::filters::HelixBendFilter::report ( std::ostream &  os,
core::pose::Pose const &  pose 
) const
overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

References filter_status_, filter_val_, threshold_, and protocols::fldsgn::TR().

core::Real protocols::fldsgn::filters::HelixBendFilter::report_sm ( core::pose::Pose const &  pose) const
overridevirtual

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute(), filter_status_, filter_val_, threshold_, and protocols::fldsgn::TR().

void protocols::fldsgn::filters::HelixBendFilter::secstruct ( std::string const &  ss)

set secondary structure

References secstruct_.

Referenced by parse_my_tag(), and set_secstruct_from_bp().

void protocols::fldsgn::filters::HelixBendFilter::set_secstruct_from_bp ( std::string const &  bp_file_path)

set secondary structure using a blueprint file

set secondary structure from blueprint

This triggers a read from disk; use with caution.

References secstruct(), and protocols::parser::BluePrint::secstruct().

Referenced by parse_my_tag().

void protocols::fldsgn::filters::HelixBendFilter::threshold ( core::Real const  r)

minimum angle for filtering

References threshold_.

Member Data Documentation

bool protocols::fldsgn::filters::HelixBendFilter::filter_status_
mutableprivate

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

core::Real protocols::fldsgn::filters::HelixBendFilter::filter_val_
mutableprivate

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

core::Size protocols::fldsgn::filters::HelixBendFilter::helix_id_
private

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

std::string protocols::fldsgn::filters::HelixBendFilter::secstruct_
mutableprivate

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

core::Real protocols::fldsgn::filters::HelixBendFilter::threshold_
private

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