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protocols::simple_filters::AtomicContactFilter Class Reference

detects atomic (<4Ang) contacts between any two atoms of two residues More...

#include <AtomicContactFilter.hh>

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

 AtomicContactFilter ()
 default ctor More...
 
 AtomicContactFilter (core::Size const res1, core::Size const res2, core::Real const distance=4.0, bool const sidechain=1, bool const backbone=0, bool const protons=0)
 Constructor with a single target residue. More...
 
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
 
 ~AtomicContactFilter () 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
 
- 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 Does this filter indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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...
 
- Public Member Functions inherited from protocols::moves::ResId
 ResId ()=default
 
 ResId (core::Size const r)
 
virtual void set_resid (core::Size const r)
 
virtual void set_resid (core::pose::ResidueIndexDescriptionCOP r)
 
virtual core::Size get_resid (core::pose::Pose const &) const
 
bool modifiable () const
 should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More...
 
void modifiable (bool const u)
 

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::ResidueSelectorOP side1_
 
core::Real distance_
 
bool sidechain_
 
bool backbone_
 
bool protons_
 

Additional Inherited Members

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

Detailed Description

detects atomic (<4Ang) contacts between any two atoms of two residues

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_filters::AtomicContactFilter::AtomicContactFilter ( )

default ctor

protocols::simple_filters::AtomicContactFilter::AtomicContactFilter ( core::Size const  res1,
core::Size const  res2,
core::Real const  distance = 4.0,
bool const  sidechain = 1,
bool const  backbone = 0,
bool const  protons = 0 
)

Constructor with a single target residue.

protocols::simple_filters::AtomicContactFilter::~AtomicContactFilter ( )
overridedefault

Member Function Documentation

bool protocols::simple_filters::AtomicContactFilter::apply ( core::pose::Pose const &  pose) const
overridevirtual
Returns
Whether a disulfide bond is possible between any of the targets

Implements protocols::filters::Filter.

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

Referenced by protocols::simple_filters::SSElementMotifContactFilter::get_SSelements_in_contact().

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

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::simple_filters::AtomicContactFilter::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 backbone_, distance_, protocols::moves::ResId::modifiable(), core::pose::parse_resnum(), protons_, protocols::moves::ResId::set_resid(), side1_, sidechain_, and protocols::simple_filters::TR().

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

Reimplemented from protocols::filters::Filter.

References compute().

Referenced by apply().

core::Real protocols::simple_filters::AtomicContactFilter::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().

Member Data Documentation

bool protocols::simple_filters::AtomicContactFilter::backbone_
private

Referenced by compute(), and parse_my_tag().

core::Real protocols::simple_filters::AtomicContactFilter::distance_
private

Referenced by apply(), and parse_my_tag().

bool protocols::simple_filters::AtomicContactFilter::protons_
private

Referenced by compute(), and parse_my_tag().

core::select::residue_selector::ResidueSelectorOP protocols::simple_filters::AtomicContactFilter::side1_
private

Referenced by compute(), and parse_my_tag().

bool protocols::simple_filters::AtomicContactFilter::sidechain_
private

Referenced by compute(), and parse_my_tag().


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