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:

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 () 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...
Public Member Functions inherited from protocols::moves::ResId
	ResId ()=default
	ResId (core::Size const r)
virtual	~ResId ()=default
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

parent

typedef protocols::filters::Filter protocols::simple_filters::AtomicContactFilter::parent

private

Constructor & Destructor Documentation

AtomicContactFilter() [1/2]

protocols::simple_filters::AtomicContactFilter::AtomicContactFilter

(

)

default ctor

AtomicContactFilter() [2/2]

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.

~AtomicContactFilter()

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

overridedefault

Member Function Documentation

apply()

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().

class_name()

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

static

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

clone()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

compute()

core::Real protocols::simple_filters::AtomicContactFilter::compute

(

core::pose::Pose const &

pose

)

const

References core::conformation::Residue::atom_begin(), core::conformation::Residue::atom_end(), backbone_, protocols::moves::ResId::get_resid(), core::select::get_residues_from_subset(), core::conformation::Residue::heavyAtoms_end(), protons_, core::pose::Pose::residue(), side1_, sidechain_, core::conformation::Residue::sidechainAtoms_begin(), and protocols::simple_filters::TR().

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

fresh_instance()

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

inlineoverridevirtual

Implements protocols::filters::Filter.

name()

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

overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

parse_my_tag()

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().

provide_xml_schema()

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

static

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

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

report()

void protocols::simple_filters::AtomicContactFilter::report ( std::ostream &  out, core::pose::Pose const &  pose  ) const

overridevirtual

Reimplemented from protocols::filters::Filter.

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

Referenced by apply().

report_sm()

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

backbone_

bool protocols::simple_filters::AtomicContactFilter::backbone_

private

Referenced by compute(), and parse_my_tag().

distance_

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

private

Referenced by apply(), and parse_my_tag().

protons_

bool protocols::simple_filters::AtomicContactFilter::protons_

private

Referenced by compute(), and parse_my_tag().

side1_

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

private

Referenced by compute(), and parse_my_tag().

sidechain_

bool protocols::simple_filters::AtomicContactFilter::sidechain_

private

Referenced by compute(), and parse_my_tag().

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

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