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protocols::simple_filters::AtomicDistanceFilter Class Reference

detects atomic contacts between two atoms of two residues More...

#include <AtomicDistanceFilter.hh>

Inheritance diagram for protocols::simple_filters::AtomicDistanceFilter:
Inheritance graph
[legend]

Public Member Functions

 AtomicDistanceFilter ()
 default ctor More...
 
 AtomicDistanceFilter (core::Size const res1, core::Size const res2, std::string const &atom_desig1="CB", std::string const &atom_desig2="CB", bool as_type1=false, bool as_type2=false, core::Real const distance=4.0)
 
bool apply (core::pose::Pose const &pose) const override
 
core::Real compute (core::pose::Pose const &pose) const
 
void report (std::ostream &out, core::pose::Pose const &pose) 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...
 
filters::FilterOP clone () const override
 
filters::FilterOP fresh_instance () const override
 
 ~AtomicDistanceFilter () override=default
 
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...
 
std::string name () const override
 
void set_selector_for_res1 (core::select::residue_selector::ResidueSelectorCOP selector1)
 
void set_selector_for_res2 (core::select::residue_selector::ResidueSelectorCOP selector2)
 
void set_atomname1 (std::string &&atomname1)
 
void set_atomname2 (std::string &&atomname2)
 
- 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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 Types

typedef protocols::filters::Filter parent
 

Private Attributes

core::select::residue_selector::ResidueSelectorCOP selector1_ = nullptr
 
core::select::residue_selector::ResidueSelectorCOP selector2_ = nullptr
 
core::pose::ResidueIndexDescriptionCOP residue1_
 
core::pose::ResidueIndexDescriptionCOP residue2_
 
std::string atomdesg1_
 
std::string atomdesg2_
 
bool astype1_
 
bool astype2_
 
core::Real distance_
 

Additional Inherited Members

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

Detailed Description

detects atomic contacts between two atoms of two residues

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_filters::AtomicDistanceFilter::AtomicDistanceFilter ( )

default ctor

protocols::simple_filters::AtomicDistanceFilter::AtomicDistanceFilter ( core::Size const  res1,
core::Size const  res2,
std::string const &  atom_desig1 = "CB",
std::string const &  atom_desig2 = "CB",
bool  as_type1 = false,
bool  as_type2 = false,
core::Real const  distance = 4.0 
)
protocols::simple_filters::AtomicDistanceFilter::~AtomicDistanceFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::AtomicDistanceFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
Returns
Whether the atom pair is within the cutoff

Implements protocols::filters::Filter.

References compute(), distance_, report(), and protocols::simple_filters::TR().

std::string protocols::simple_filters::AtomicDistanceFilter::class_name ( )
static
filters::FilterOP protocols::simple_filters::AtomicDistanceFilter::clone ( ) const
inlineoverridevirtual
core::Real protocols::simple_filters::AtomicDistanceFilter::compute ( core::pose::Pose const &  pose) const
filters::FilterOP protocols::simple_filters::AtomicDistanceFilter::fresh_instance ( ) const
inlineoverridevirtual
std::string protocols::simple_filters::AtomicDistanceFilter::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::AtomicDistanceFilter::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 astype1_, astype2_, atomdesg1_, atomdesg2_, distance_, core::select::residue_selector::parse_residue_selector(), core::pose::parse_resnum(), residue1_, residue2_, selector1_, selector2_, and protocols::simple_filters::TR().

void protocols::simple_filters::AtomicDistanceFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_filters::AtomicDistanceFilter::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References astype1_, astype2_, atomdesg1_, atomdesg2_, and compute().

Referenced by apply().

core::Real protocols::simple_filters::AtomicDistanceFilter::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 compute().

void protocols::simple_filters::AtomicDistanceFilter::set_atomname1 ( std::string &&  atomname1)
inline

References astype1_, and atomdesg1_.

void protocols::simple_filters::AtomicDistanceFilter::set_atomname2 ( std::string &&  atomname2)
inline

References astype2_, and atomdesg2_.

void protocols::simple_filters::AtomicDistanceFilter::set_selector_for_res1 ( core::select::residue_selector::ResidueSelectorCOP  selector1)
inline

References selector1_.

void protocols::simple_filters::AtomicDistanceFilter::set_selector_for_res2 ( core::select::residue_selector::ResidueSelectorCOP  selector2)
inline

References selector2_.

Member Data Documentation

bool protocols::simple_filters::AtomicDistanceFilter::astype1_
private
bool protocols::simple_filters::AtomicDistanceFilter::astype2_
private
std::string protocols::simple_filters::AtomicDistanceFilter::atomdesg1_
private
std::string protocols::simple_filters::AtomicDistanceFilter::atomdesg2_
private
core::Real protocols::simple_filters::AtomicDistanceFilter::distance_
private

Referenced by apply(), and parse_my_tag().

core::pose::ResidueIndexDescriptionCOP protocols::simple_filters::AtomicDistanceFilter::residue1_
private

Referenced by compute(), and parse_my_tag().

core::pose::ResidueIndexDescriptionCOP protocols::simple_filters::AtomicDistanceFilter::residue2_
private

Referenced by compute(), and parse_my_tag().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::AtomicDistanceFilter::selector1_ = nullptr
private
core::select::residue_selector::ResidueSelectorCOP protocols::simple_filters::AtomicDistanceFilter::selector2_ = nullptr
private

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