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

#include <FragmentLookupFilter.hh>

Inheritance diagram for protocols::indexed_structure_store::filters::FragmentLookupFilter:

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
void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...
Public Member Functions inherited from protocols::filters::Filter
	Filter ()
	Filter (std::string 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)

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

DataMap

typedef basic::datacache::DataMap protocols::indexed_structure_store::filters::FragmentLookupFilter::DataMap

FilterOP

typedef protocols::filters::FilterOP protocols::indexed_structure_store::filters::FragmentLookupFilter::FilterOP

FragmentLookupOP

typedef protocols::indexed_structure_store::FragmentLookupOP protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupOP

FragmentLookupResult

typedef protocols::indexed_structure_store::FragmentLookupResult protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupResult

FragmentSpecification

typedef protocols::indexed_structure_store::FragmentSpecification protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentSpecification

Pose

typedef core::pose::Pose protocols::indexed_structure_store::filters::FragmentLookupFilter::Pose

Real

typedef core::Real protocols::indexed_structure_store::filters::FragmentLookupFilter::Real

Size

typedef core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::Size

TagPtr

typedef utility::tag::TagPtr protocols::indexed_structure_store::filters::FragmentLookupFilter::TagPtr

Constructor & Destructor Documentation

FragmentLookupFilter() [1/4]

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

Construct targeting the given named lookup in the default backend.

FragmentLookupFilter() [2/4]

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.

FragmentLookupFilter() [3/4]

protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter

(

FragmentLookupFilter const &

rval

)

~FragmentLookupFilter()

protocols::indexed_structure_store::filters::FragmentLookupFilter::~FragmentLookupFilter ( )

inlineoverride

FragmentLookupFilter() [4/4]

protocols::indexed_structure_store::filters::FragmentLookupFilter::FragmentLookupFilter ( )

protected

Referenced by clone(), and fresh_instance().

Member Function Documentation

apply()

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(), threshold_, and protocols::indexed_structure_store::filters::TR().

class_name()

std::string protocols::indexed_structure_store::filters::FragmentLookupFilter::class_name ( )

static

Referenced by protocols::indexed_structure_store::filters::FragmentLookupFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

FilterOP protocols::indexed_structure_store::filters::FragmentLookupFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References FragmentLookupFilter().

compute()

core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::compute

(

core::pose::Pose const &

pose

)

const

References b_target_chain_, cached_lookup_result_, core::pose::Pose::conformation(), protocols::indexed_structure_store::filters::First, lookup_mode_, lookup_result(), core::conformation::Conformation::num_chains(), core::pose::Pose::size(), core::pose::Pose::split_by_chain(), target_chain_, target_lookup_, and protocols::indexed_structure_store::filters::TR().

Referenced by apply().

fragment_specification()

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

(

)

References target_lookup_.

fresh_instance()

FilterOP protocols::indexed_structure_store::filters::FragmentLookupFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

References FragmentLookupFilter().

lookup_result()

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

inline

References cached_lookup_result_.

Referenced by compute().

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

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_, threshold_, and protocols::indexed_structure_store::filters::TR().

provide_citation_info()

void protocols::indexed_structure_store::filters::FragmentLookupFilter::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::filters::Filter.

provide_xml_schema()

void protocols::indexed_structure_store::filters::FragmentLookupFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::indexed_structure_store::filters::FragmentLookupFilterCreator::provide_xml_schema().

report()

void protocols::indexed_structure_store::filters::FragmentLookupFilter::report ( std::ostream &  os, core::pose::Pose const &    ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References cached_lookup_result_, and core::id::to_string().

report_sm()

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(), core::id::to_string(), and protocols::indexed_structure_store::filters::TR().

set_chain()

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

inline

sets chain

References target_chain_.

Friends And Related Function Documentation

FragmentLookupFilterCreator

friend class FragmentLookupFilterCreator

friend

Member Data Documentation

b_target_chain_

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

private

Referenced by compute(), and parse_my_tag().

cached_lookup_result_

std::map<core::Size, FragmentLookupResult> protocols::indexed_structure_store::filters::FragmentLookupFilter::cached_lookup_result_

mutableprivate

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

lookup_mode_

LookupMode protocols::indexed_structure_store::filters::FragmentLookupFilter::lookup_mode_

private

Referenced by compute(), and parse_my_tag().

target_chain_

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

private

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

target_lookup_

FragmentLookupOP protocols::indexed_structure_store::filters::FragmentLookupFilter::target_lookup_

private

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

threshold_

core::Size protocols::indexed_structure_store::filters::FragmentLookupFilter::threshold_

private

Referenced by apply(), and parse_my_tag().

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

• src/protocols/indexed_structure_store/filters/FragmentLookupFilter.hh
• src/protocols/indexed_structure_store/filters/FragmentLookupFilter.cc