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protocols::fldsgn::filters::StrandCurvatureByLevels Class Reference

Newer version of filter used in Marcos & Basanta et al. 2017. More...

#include <StrandCurvatureByLevels.hh>

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

Public Types

typedef core::Real Real
 
typedef protocols::filters::Filter Super
 
typedef protocols::filters::Filter Filter
 
typedef std::string String
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef core::pose::Pose Pose
 
typedef
protocols::fldsgn::topology::StrandPairingSet 
StrandPairingSet
 
typedef
protocols::fldsgn::topology::StrandPairingSetOP 
StrandPairingSetOP
 
typedef
protocols::fldsgn::topology::SS_Info2 
SS_Info2
 
typedef
protocols::fldsgn::topology::SS_Info2_OP 
SS_Info2_OP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 StrandCurvatureByLevels ()
 
 ~StrandCurvatureByLevels () override
 
bool apply (core::pose::Pose const &pose) const override
 returns true if the structure passes the filter, false otherwise 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...
 
void secstruct (String const &ss)
 miniimum angle for filtering More...
 
void bend_level (core::Size const r)
 
void filter_min_bend (Real const r)
 miniimum angle for filtering More...
 
void filter_max_bend (Real const r)
 maximum angle for filtering More...
 
void twist_level (core::Size const r)
 
void filter_min_twist (Real const r)
 miniimum twist for filtering More...
 
void filter_max_twist (Real const r)
 maximum twist for filtering More...
 
void strand_id (core::Size const r)
 miniimum angle for filtering More...
 
void output_type (String const &s)
 set output type More...
 
void concavity_reference_residue (String const &ss)
 
void concavity_direction (bool const &r)
 
virtual core::Real compute (Pose const &pose) const
 
- 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

String secstruct_
 if value is empty, dssp will run for ss definition ( default is emptry ) More...
 
core::Size bend_level_
 
Real filter_min_bend_
 filtered min angle between helix and sheet More...
 
Real filter_max_bend_
 filtered max angle between helix and sheet More...
 
core::Size twist_level_
 
Real filter_min_twist_
 filtered min twist between helix and sheet More...
 
Real filter_max_twist_
 filtered max twist between helix and sheet More...
 
core::Size strand_id_
 strand id More...
 
String output_type_
 output_type More...
 
Real output_value_
 output value, the result of filterring calculation More...
 
String concavity_reference_residue_
 
bool concavity_direction_
 

Additional Inherited Members

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

Detailed Description

Newer version of filter used in Marcos & Basanta et al. 2017.

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

bool protocols::fldsgn::filters::StrandCurvatureByLevels::apply ( core::pose::Pose const &  pose) const
overridevirtual
void protocols::fldsgn::filters::StrandCurvatureByLevels::bend_level ( core::Size const  r)

References bend_level_.

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

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

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

References apply(), and output_value_.

Referenced by report_sm().

void protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_direction ( bool const &  r)

References concavity_direction_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_reference_residue ( String const &  ss)
void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_bend ( core::Real const  r)

maximum angle for filtering

References filter_max_bend_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_twist ( core::Real const  r)

maximum twist for filtering

References filter_max_twist_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_bend ( core::Real const  r)

miniimum angle for filtering

minimum angle for filtering

References filter_min_bend_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_twist ( core::Real const  r)

miniimum twist for filtering

References filter_min_twist_.

protocols::filters::FilterOP protocols::fldsgn::filters::StrandCurvatureByLevels::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Implements protocols::filters::Filter.

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

Reimplemented from protocols::filters::Filter.

References class_name().

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

set output type

References output_type_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::fldsgn::filters::StrandCurvatureByLevels::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::fldsgn::filters::StrandCurvatureByLevels::report ( std::ostream &  os,
core::pose::Pose const &  pose 
) const
overridevirtual

allows printing data to a stream

Reimplemented from protocols::filters::Filter.

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

required for reporting score values

Reimplemented from protocols::filters::Filter.

References compute().

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

miniimum angle for filtering

References secstruct_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::strand_id ( core::Size const  r)

miniimum angle for filtering

Strand id number.

References strand_id_.

void protocols::fldsgn::filters::StrandCurvatureByLevels::twist_level ( core::Size const  r)

References twist_level_.

Member Data Documentation

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::bend_level_
private

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

bool protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_direction_
private
String protocols::fldsgn::filters::StrandCurvatureByLevels::concavity_reference_residue_
private
Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_bend_
private

filtered max angle between helix and sheet

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_max_twist_
private

filtered max twist between helix and sheet

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_bend_
private

filtered min angle between helix and sheet

Referenced by filter_min_bend(), and parse_my_tag().

Real protocols::fldsgn::filters::StrandCurvatureByLevels::filter_min_twist_
private

filtered min twist between helix and sheet

Referenced by filter_min_twist(), and parse_my_tag().

String protocols::fldsgn::filters::StrandCurvatureByLevels::output_type_
private

output_type

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

Real protocols::fldsgn::filters::StrandCurvatureByLevels::output_value_
mutableprivate

output value, the result of filterring calculation

Referenced by apply(), and compute().

String protocols::fldsgn::filters::StrandCurvatureByLevels::secstruct_
mutableprivate

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

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

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::strand_id_
private

strand id

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

core::Size protocols::fldsgn::filters::StrandCurvatureByLevels::twist_level_
private

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


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