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

#include <AtomicContactFilter.hh>

Inheritance diagram for protocols::simple_filters::AtomicContactFilter:

Collaboration 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...

virtual bool	apply (core::pose::Pose const &pose) const

core::Real	compute (core::pose::Pose const &pose) const

virtual void	report (std::ostream &out, core::pose::Pose const &pose) const

virtual core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...

virtual filters::FilterOP	clone () const

virtual filters::FilterOP	fresh_instance () const

virtual	~AtomicContactFilter ()

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)

Public Member Functions inherited from protocols::filters::Filter
	Filter ()

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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 void	apply (core::io::serialization::PipeMap &pmap)

virtual void	score (core::io::serialization::PipeMap &pmap)

virtual core::Real	score (core::pose::Pose &pose)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)

virtual std::string	name () const

Public Member Functions inherited from protocols::moves::ResId
	ResId ()

	ResId (core::Size const r)

virtual void	set_resid (core::Size const r)

virtual core::Size	get_resid () const

virtual core::Size &	get_resid ()

virtual bool	modifiable () const
	should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More...

virtual void	modifiable (bool const u)

virtual	~ResId ()

Private Types
typedef protocols::filters::Filter	parent

Private Attributes
core::Size	residue1_

utility::vector1< core::Size >	range1_

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

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

private

Constructor & Destructor Documentation

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

default ctor

Referenced by clone(), protocols::simple_filters::AtomicContactFilterCreator::create_filter(), and fresh_instance().

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.

References range1_, and residue1_.

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

inlinevirtual

Member Function Documentation

bool protocols::simple_filters::AtomicContactFilter::apply ( core::pose::Pose const & pose) const

virtual

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().

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

inlinevirtual

Implements protocols::filters::Filter.

References AtomicContactFilter().

core::Real protocols::simple_filters::AtomicContactFilter::compute ( core::pose::Pose const & pose) const

References backbone_, protocols::moves::ResId::get_resid(), protons_, range1_, core::pose::Pose::residue(), sidechain_, core::conformation::Residue::sidechainAtoms_begin(), and protocols::simple_filters::TR().

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

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

inlinevirtual

Implements protocols::filters::Filter.

References AtomicContactFilter().

void protocols::simple_filters::AtomicContactFilter::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)