#include <AlaScan.hh>

Inheritance diagram for protocols::simple_filters::AlaScan:

Collaboration diagram for protocols::simple_filters::AlaScan:

Public Member Functions
	AlaScan ()

	AlaScan (bool const chain1, bool const chain2, core::Size const repeats, core::Real const dist, core::scoring::ScoreFunctionCOP scorefxn, core::Size const jump, bool const symmetry)

bool	apply (core::pose::Pose const &) const
	Returns true if the given pose passes the filter, false otherwise. More...

filters::FilterOP	clone () const

filters::FilterOP	fresh_instance () const

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

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

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

void	chain1 (bool const c1)

void	chain2 (bool const c2)

void	dist (core::Real const d)

void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)

core::Real	ddG_for_single_residue (core::pose::Pose const &pose, core::Size const resi) const

bool	chain1 () const

bool	chain2 () const

core::Size	repeats () const

void	repeats (core::Size const r)

core::Size	jump () const

void	jump (core::Size const j)

core::Real	dist () const

virtual	~AlaScan ()

void	repack (bool const repack)

bool	repack () const

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, 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

Private Attributes
bool	chain1_

bool	chain2_

core::Size	repeats_

core::Real	distance_threshold_

core::Size	jump_

bool	symmetry_

core::scoring::ScoreFunctionOP	scorefxn_

bool	repack_

Additional Inherited Members
Protected Attributes inherited from protocols::filters::Filter
std::string	scorename_

Constructor & Destructor Documentation

protocols::simple_filters::AlaScan::AlaScan ( )

inline

Referenced by clone(), and fresh_instance().

protocols::simple_filters::AlaScan::AlaScan	(	bool const	chain1,
		bool const	chain2,
		core::Size const	repeats,
		core::Real const	dist,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	jump = `1`,
		bool const	symmetry = `false`
	)

References scorefxn_, and symmetry_.

protocols::simple_filters::AlaScan::~AlaScan ( )

virtual

Member Function Documentation

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

inlinevirtual

Returns true if the given pose passes the filter, false otherwise.

Implements protocols::filters::Filter.

void protocols::simple_filters::AlaScan::chain1 ( bool const c1)

inline

References chain1_.

bool protocols::simple_filters::AlaScan::chain1 ( ) const

inline

References chain1_.

void protocols::simple_filters::AlaScan::chain2 ( bool const c2)

inline

References chain2_.

bool protocols::simple_filters::AlaScan::chain2 ( ) const

inline

References chain2_.

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

inlinevirtual

Implements protocols::filters::Filter.

References AlaScan().

core::Real protocols::simple_filters::AlaScan::ddG_for_single_residue	(	core::pose::Pose const &	pose,
		core::Size const	resi
	)		const

References core::chemical::aa_ala, protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::DdgFilter::compute(), core::conformation::Residue::is_protein(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), protocols::simple_filters::DdgFilter::repack(), repack(), repeats_, core::pose::Pose::residue(), scorefxn_, core::pose::Pose::total_residue(), core::scoring::total_score, and protocols::simple_filters::TR().

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), and report().

void protocols::simple_filters::AlaScan::dist ( core::Real const d)

inline

References distance_threshold_.

core::Real protocols::simple_filters::AlaScan::dist ( ) const

inline

References distance_threshold_.

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

inlinevirtual

Implements protocols::filters::Filter.

References AlaScan().

core::Size protocols::simple_filters::AlaScan::jump ( ) const

inline

References jump_.

Referenced by protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), and protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

void protocols::simple_filters::AlaScan::jump ( core::Size const j)

inline

References jump_.

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