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protocols::simple_filters::ResidueDepthFilter Class Reference

#include <ResidueDepthFilter.hh>

Inheritance diagram for protocols::simple_filters::ResidueDepthFilter:
Inheritance graph
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Public Member Functions

 ResidueDepthFilter ()
 Filter. More...
 
 ~ResidueDepthFilter () override
 
bool apply (core::pose::Pose const &) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
core::Real get_SDE_score (core::pose::Pose const &pose)
 
utility::vector1< core::Realget_residue_depth (core::pose::Pose const &pose) const
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
void set_report_crd (bool const value)
 
void set_niter (core::Size const value)
 
std::string name () const override
 
utility::vector1< core::Realget_scdepth_avrg () const
 
utility::vector1< core::Realget_scdepth_sdev () const
 
utility::vector1< core::Realget_scdepth_fvar () const
 
- 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 core::Real report_sm (core::pose::Pose const &) const
 used to report filter internals through a score or silent file More...
 
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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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

void initialize ()
 
void read_db (std::string const infile)
 
void read_GUIP_matrix (std::string const infile)
 
void fill_GUIP ()
 
utility::vector1< core::Sizeget_n8 (core::pose::Pose const &pose) const
 
utility::vector1< core::Sizesearch_close_frags (utility::vector1< core::Vector > const &frag_crd, core::Size const n8, core::Size const npick) const
 
core::Real get_residue_similarity (core::conformation::Residue const &rsd, utility::vector1< core::Vector > const &frag_crd, core::Size const n8, utility::vector1< ResidueDepthDataCOP > const context_rdd, utility::vector1< core::Size > const &close_ids, core::Size const n) const
 
core::Real get_simscore (core::chemical::AA const aa1, core::chemical::AA const aa2) const
 
core::Real compare_by_superposition (utility::vector1< ResidueDepthDataCOP > const &context_rdd, utility::vector1< core::Vector > const &frag_crd, utility::vector1< ResidueDepthDataCOP > const &context_rdd_ref, utility::vector1< core::Vector > const &frag_crd_ref) const
 
utility::vector1
< ResidueDepthDataCOP
make_context (core::pose::Pose const &pose, core::Size const ires) const
 
utility::vector1
< ResidueDepthDataCOP
make_context_ref (core::Size const ipdb, core::Size const ires) const
 
void fill_neighs (ResidueDepthData &rdd, utility::vector1< ResidueDepthData > const &pdb_rdds) const
 

Private Attributes

std::string dbfile_
 
std::string GUIP_matrix_file_
 
ResidueDepthCalculator RDC_
 
core::Size ncandidate1_
 
core::Size ncandidate2_
 
std::string similarity_mode_
 
core::Real gamma_
 
utility::vector1
< utility::vector1
< ResidueDepthDataCOP > > 
db_
 
utility::vector1< std::string > pdbid_
 
std::map< core::Size,
utility::vector1
< ResidueDepthFrag > > 
frag_db_
 
utility::vector1
< utility::vector1< core::Real > > 
GUIP_matrix_
 
core::select::residue_selector::ResidueSelectorCOP evalres_
 
core::Real maxdist_
 
core::Real mindist_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_filters::ResidueDepthFilter::ResidueDepthFilter ( )

Filter.

References initialize().

protocols::simple_filters::ResidueDepthFilter::~ResidueDepthFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::ResidueDepthFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
std::string protocols::simple_filters::ResidueDepthFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::ResidueDepthFilter::clone ( ) const
inlineoverridevirtual
core::Real protocols::simple_filters::ResidueDepthFilter::compare_by_superposition ( utility::vector1< ResidueDepthDataCOP > const &  context_rdd,
utility::vector1< core::Vector > const &  frag_crd,
utility::vector1< ResidueDepthDataCOP > const &  context_rdd_ref,
utility::vector1< core::Vector > const &  frag_crd_ref 
) const
private
void protocols::simple_filters::ResidueDepthFilter::fill_GUIP ( )
private
void protocols::simple_filters::ResidueDepthFilter::fill_neighs ( ResidueDepthData rdd,
utility::vector1< ResidueDepthData > const &  pdb_rdds 
) const
private
filters::FilterOP protocols::simple_filters::ResidueDepthFilter::fresh_instance ( ) const
inlineoverridevirtual
utility::vector1< core::Size > protocols::simple_filters::ResidueDepthFilter::get_n8 ( core::pose::Pose const &  pose) const
private
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_residue_depth ( core::pose::Pose const &  pose) const
core::Real protocols::simple_filters::ResidueDepthFilter::get_residue_similarity ( core::conformation::Residue const &  rsd,
utility::vector1< core::Vector > const &  frag_crd,
core::Size const  n8,
utility::vector1< ResidueDepthDataCOP > const  context_rdd,
utility::vector1< core::Size > const &  close_ids,
core::Size const  n 
) const
private
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_avrg ( ) const
inline
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_fvar ( ) const
inline
utility::vector1< core::Real > protocols::simple_filters::ResidueDepthFilter::get_scdepth_sdev ( ) const
inline
core::Real protocols::simple_filters::ResidueDepthFilter::get_SDE_score ( core::pose::Pose const &  pose)
core::Real protocols::simple_filters::ResidueDepthFilter::get_simscore ( core::chemical::AA const  aa1,
core::chemical::AA const  aa2 
) const
private
void protocols::simple_filters::ResidueDepthFilter::initialize ( )
private
utility::vector1< ResidueDepthDataCOP > protocols::simple_filters::ResidueDepthFilter::make_context ( core::pose::Pose const &  pose,
core::Size const  ires 
) const
private
utility::vector1< ResidueDepthDataCOP > protocols::simple_filters::ResidueDepthFilter::make_context_ref ( core::Size const  ipdb,
core::Size const  ires 
) const
private

References db_.

Referenced by get_residue_similarity().

std::string protocols::simple_filters::ResidueDepthFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::ResidueDepthFilter::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual

Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing.

Reimplemented from protocols::filters::Filter.

References evalres_, maxdist_, mindist_, RDC_, protocols::simple_filters::ResidueDepthCalculator::set_dcut1(), and protocols::simple_filters::ResidueDepthCalculator::set_dcut2().

void protocols::simple_filters::ResidueDepthFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::ResidueDepthFilter::read_db ( std::string const  infile)
private
void protocols::simple_filters::ResidueDepthFilter::read_GUIP_matrix ( std::string const  infile)
private

References GUIP_matrix_, and protocols::hybridization::val.

Referenced by initialize().

utility::vector1< core::Size > protocols::simple_filters::ResidueDepthFilter::search_close_frags ( utility::vector1< core::Vector > const &  frag_crd,
core::Size const  n8,
core::Size const  npick 
) const
private
void protocols::simple_filters::ResidueDepthFilter::set_niter ( core::Size const  value)
inline
void protocols::simple_filters::ResidueDepthFilter::set_report_crd ( bool const  value)
inline

Member Data Documentation

utility::vector1< utility::vector1< ResidueDepthDataCOP > > protocols::simple_filters::ResidueDepthFilter::db_
private
std::string protocols::simple_filters::ResidueDepthFilter::dbfile_
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::ResidueDepthFilter::evalres_
private

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

std::map< core::Size, utility::vector1<ResidueDepthFrag> > protocols::simple_filters::ResidueDepthFilter::frag_db_
private
core::Real protocols::simple_filters::ResidueDepthFilter::gamma_
private
utility::vector1< utility::vector1< core::Real > > protocols::simple_filters::ResidueDepthFilter::GUIP_matrix_
private

Referenced by get_simscore(), and read_GUIP_matrix().

std::string protocols::simple_filters::ResidueDepthFilter::GUIP_matrix_file_
private

Referenced by initialize().

core::Real protocols::simple_filters::ResidueDepthFilter::maxdist_
private

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

core::Real protocols::simple_filters::ResidueDepthFilter::mindist_
private

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

core::Size protocols::simple_filters::ResidueDepthFilter::ncandidate1_
private

Referenced by get_SDE_score(), and initialize().

core::Size protocols::simple_filters::ResidueDepthFilter::ncandidate2_
private

Referenced by get_SDE_score(), and initialize().

utility::vector1< std::string > protocols::simple_filters::ResidueDepthFilter::pdbid_
private

Referenced by get_residue_similarity(), and read_db().

ResidueDepthCalculator protocols::simple_filters::ResidueDepthFilter::RDC_
private
std::string protocols::simple_filters::ResidueDepthFilter::similarity_mode_
private

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