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protocols::indexed_structure_store::filters::FragmentLookupFilter Class Reference

#include <FragmentLookupFilter.hh>

Inheritance diagram for protocols::indexed_structure_store::filters::FragmentLookupFilter:
Inheritance graph
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Public Types

typedef
protocols::indexed_structure_store::FragmentLookupOP 
FragmentLookupOP
 
typedef
protocols::indexed_structure_store::FragmentLookupResult 
FragmentLookupResult
 
typedef
protocols::indexed_structure_store::FragmentSpecification 
FragmentSpecification
 
typedef core::Real Real
 
typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef utility::tag::TagPtr TagPtr
 
typedef
protocols::filters::FilterOP 
FilterOP
 
typedef basic::datacache::DataMap DataMap
 

Public Member Functions

 FragmentLookupFilter (std::string lookup_name, LookupMode mode=First)
 Construct targeting the given named lookup in the default backend. More...
 
 FragmentLookupFilter (std::string lookup_name, std::string store_path, LookupMode mode=First, core::Size target_chain=0, core::Size threshold=0, bool b_target_chain=false)
 Construct targeting the given lookup in the given backend. More...
 
 FragmentLookupFilter (FragmentLookupFilter const &rval)
 
 ~FragmentLookupFilter () override
 
FilterOP clone () const override
 
FilterOP fresh_instance () const override
 
bool apply (Pose const &pose) const override
 Returns true if the given pose passes the filter, false otherwise. More...
 
void parse_my_tag (utility::tag::TagCOP tag, DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
core::Size compute (core::pose::Pose const &pose) const
 
void report (std::ostream &, core::pose::Pose const &) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
std::map< core::Size,
FragmentLookupResult > const & 
lookup_result ()
 
FragmentSpecification const & fragment_specification ()
 
void set_chain (core::Size const chainid)
 sets chain More...
 
std::string name () const override
 
bool filter_provides_citation_info () const override
 Does this filter provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation (Dang et al 2017). 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_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)
 

Protected Member Functions

 FragmentLookupFilter ()
 

Private Attributes

FragmentLookupOP target_lookup_
 
std::map< core::Size,
FragmentLookupResult
cached_lookup_result_
 
LookupMode lookup_mode_
 
core::Size target_chain_
 
core::Size threshold_
 
bool b_target_chain_
 

Friends

class FragmentLookupFilterCreator
 

Additional Inherited Members

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

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter ( std::string  lookup_name,
LookupMode  mode = First 
)

Construct targeting the given named lookup in the default backend.

protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter ( std::string  lookup_name,
std::string  store_path,
LookupMode  mode = First,
core::Size  target_chain = 0,
core::Size  threshold = 0,
bool  b_target_chain = false 
)

Construct targeting the given lookup in the given backend.

protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter ( FragmentLookupFilter const &  rval)
protocols::indexed_structure_store::filters::FragmentLookupFilter::~FragmentLookupFilter ( )
inlineoverride
protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter ( )
protected

Referenced by clone(), and fresh_instance().

Member Function Documentation

bool protocols::indexed_structure_store::filters::FragmentLookupFilter::apply ( Pose const &  pose) const
overridevirtual

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

Implements protocols::filters::Filter.

References compute(), and threshold_.

std::string protocols::indexed_structure_store::filters::FragmentLookupFilter::class_name ( )
static
FilterOP protocols::indexed_structure_store::filters::FragmentLookupFilter::clone ( ) const
inlineoverridevirtual
core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::compute ( core::pose::Pose const &  pose) const
bool protocols::indexed_structure_store::filters::FragmentLookupFilter::filter_provides_citation_info ( ) const
overridevirtual

Does this filter provide information about how to cite it?

Returns true.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::filters::Filter.

FragmentSpecification const & protocols::indexed_structure_store::filters::FragmentLookupFilter::fragment_specification ( )

References target_lookup_.

FilterOP protocols::indexed_structure_store::filters::FragmentLookupFilter::fresh_instance ( ) const
inlineoverridevirtual
std::map<core::Size, FragmentLookupResult> const& protocols::indexed_structure_store::filters::FragmentLookupFilter::lookup_result ( )
inline

References cached_lookup_result_.

Referenced by compute().

std::string protocols::indexed_structure_store::filters::FragmentLookupFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::indexed_structure_store::filters::FragmentLookupFilter::parse_my_tag ( utility::tag::TagCOP  ,
DataMap  
)
overridevirtual

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

Reimplemented from protocols::filters::Filter.

References b_target_chain_, protocols::indexed_structure_store::filters::Closest, protocols::indexed_structure_store::filters::First, lookup_mode_, target_chain_, target_lookup_, and threshold_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::indexed_structure_store::filters::FragmentLookupFilter::provide_citation_info ( ) const
overridevirtual

Provide the citation (Dang et al 2017).

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::filters::Filter.

void protocols::indexed_structure_store::filters::FragmentLookupFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::indexed_structure_store::filters::FragmentLookupFilter::report ( std::ostream &  os,
core::pose::Pose const &   
) const
overridevirtual
core::Real protocols::indexed_structure_store::filters::FragmentLookupFilter::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References cached_lookup_result_, core::pose::Pose::size(), and core::id::to_string().

void protocols::indexed_structure_store::filters::FragmentLookupFilter::set_chain ( core::Size const  chainid)
inline

sets chain

References target_chain_.

Friends And Related Function Documentation

friend class FragmentLookupFilterCreator
friend

Member Data Documentation

bool protocols::indexed_structure_store::filters::FragmentLookupFilter::b_target_chain_
private

Referenced by compute(), and parse_my_tag().

std::map<core::Size, FragmentLookupResult> protocols::indexed_structure_store::filters::FragmentLookupFilter::cached_lookup_result_
mutableprivate
LookupMode protocols::indexed_structure_store::filters::FragmentLookupFilter::lookup_mode_
private

Referenced by compute(), and parse_my_tag().

core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::target_chain_
private

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

FragmentLookupOP protocols::indexed_structure_store::filters::FragmentLookupFilter::target_lookup_
private
core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::threshold_
private

Referenced by apply(), and parse_my_tag().


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