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:

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 () 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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

parent

typedef protocols::filters::Filter protocols::simple_filters::AtomicDistanceFilter::parent

private

Constructor & Destructor Documentation

AtomicDistanceFilter() [1/2]

protocols::simple_filters::AtomicDistanceFilter::AtomicDistanceFilter

(

)

default ctor

AtomicDistanceFilter() [2/2]

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
	)

~AtomicDistanceFilter()

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

overridedefault

Member Function Documentation

apply()

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().

class_name()

std::string protocols::simple_filters::AtomicDistanceFilter::class_name ( )

static

Referenced by protocols::simple_filters::AtomicDistanceFilterCreator::keyname(), name(), and provide_xml_schema().

clone()

filters::FilterOP protocols::simple_filters::AtomicDistanceFilter::clone ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::AtomicDistanceFilter::compute

(

core::pose::Pose const &

pose

)

const

References astype1_, astype2_, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_type(), atomdesg1_, atomdesg2_, core::chemical::ResidueType::has(), core::chemical::ResidueTypeBase::name(), core::chemical::AtomType::name(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), residue1_, residue2_, selector1_, selector2_, core::conformation::Residue::seqpos(), protocols::simple_filters::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().

Referenced by apply(), report(), and report_sm().

fresh_instance()

filters::FilterOP protocols::simple_filters::AtomicDistanceFilter::fresh_instance ( ) const

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

std::string protocols::simple_filters::AtomicDistanceFilter::name ( ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

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().

provide_xml_schema()

void protocols::simple_filters::AtomicDistanceFilter::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::pose::attributes_for_parse_resnum(), class_name(), and protocols::filters::xsd_type_definition_w_attributes().

Referenced by protocols::simple_filters::AtomicDistanceFilterCreator::provide_xml_schema().

report()

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_, compute(), and core::conformation::membrane::out.

Referenced by apply().

report_sm()

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().

set_atomname1()

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

inline

References astype1_, and atomdesg1_.

set_atomname2()

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

inline

References astype2_, and atomdesg2_.

set_selector_for_res1()

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

inline

References selector1_.

set_selector_for_res2()

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

inline

References selector2_.

Member Data Documentation

astype1_

bool protocols::simple_filters::AtomicDistanceFilter::astype1_

private

Referenced by compute(), parse_my_tag(), report(), and set_atomname1().

astype2_

bool protocols::simple_filters::AtomicDistanceFilter::astype2_

private

Referenced by compute(), parse_my_tag(), report(), and set_atomname2().

atomdesg1_

std::string protocols::simple_filters::AtomicDistanceFilter::atomdesg1_

private

Referenced by compute(), parse_my_tag(), report(), and set_atomname1().

atomdesg2_

std::string protocols::simple_filters::AtomicDistanceFilter::atomdesg2_

private

Referenced by compute(), parse_my_tag(), report(), and set_atomname2().

distance_

core::Real protocols::simple_filters::AtomicDistanceFilter::distance_

private

Referenced by apply(), and parse_my_tag().

residue1_

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

private

Referenced by compute(), and parse_my_tag().

residue2_

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

private

Referenced by compute(), and parse_my_tag().

selector1_

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

private

Referenced by compute(), parse_my_tag(), and set_selector_for_res1().

selector2_

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

private

Referenced by compute(), parse_my_tag(), and set_selector_for_res2().

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

• src/protocols/simple_filters/AtomicDistanceFilter.hh
• src/protocols/simple_filters/AtomicDistanceFilter.cc