protocols::simple_filters::AlaScan Class Reference

#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_

Detailed Description

Definition at line 36 of file AlaScan.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 39 of file AlaScan.hh.

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
	)

Definition at line 78 of file AlaScan.cc.

References scorefxn_, and symmetry_.

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

virtual

Definition at line 91 of file AlaScan.cc.

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.

Definition at line 41 of file AlaScan.hh.

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

inline

Definition at line 52 of file AlaScan.hh.

References chain1_.

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

inline

Definition at line 57 of file AlaScan.hh.

References chain1_.

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

inline

Definition at line 53 of file AlaScan.hh.

References chain2_.

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

inline

Definition at line 58 of file AlaScan.hh.

References chain2_.

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

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 42 of file AlaScan.hh.

References AlaScan().

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

Definition at line 131 of file AlaScan.cc.

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

Definition at line 54 of file AlaScan.hh.

References distance_threshold_.

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

inline

Definition at line 63 of file AlaScan.hh.

References distance_threshold_.

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

inlinevirtual

Implements protocols::filters::Filter.

Definition at line 45 of file AlaScan.hh.

References AlaScan().

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

inline

Definition at line 61 of file AlaScan.hh.

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

Definition at line 62 of file AlaScan.hh.

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 &    )

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 97 of file parse_filters.cc.

References protocols::moves::DataMap::get(), and core::TR().

void protocols::simple_filters::AlaScan::repack

(

bool const

repack)

Definition at line 100 of file AlaScan.cc.

References repack(), and repack_.

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

bool protocols::simple_filters::AlaScan::repack

(

)

const

Definition at line 94 of file AlaScan.cc.

References repack_.

Referenced by ddG_for_single_residue(), and repack().

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

inline

Definition at line 59 of file AlaScan.hh.

References repeats_.

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

void protocols::simple_filters::AlaScan::repeats ( core::Size const  r)

inline

Definition at line 60 of file AlaScan.hh.

References repeats_.

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

virtual

Reimplemented from protocols::filters::Filter.

Definition at line 173 of file AlaScan.cc.

References protocols::simple_filters::ScoreTypeFilter::compute(), protocols::simple_filters::DdgFilter::compute(), core::pose::Pose::conformation(), ddG_for_single_residue(), distance_threshold_, core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), core::conformation::Residue::is_protein(), protocols::scoring::Interface::jump(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), repeats_, report_symmetry(), core::pose::Pose::residue(), scorefxn_, core::pose::Pose::total_residue(), core::scoring::total_score, core::pose::Pose::update_residue_neighbors(), and core::kinematics::FoldTree::upstream_jump_residue().

core::Real protocols::simple_filters::AlaScan::report_sm ( core::pose::Pose const &  ) const

inlinevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

Definition at line 51 of file AlaScan.hh.

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

Definition at line 223 of file AlaScan.cc.

References core::chemical::aa_ala, protocols::scoring::Interface::calculate(), protocols::simple_filters::DdgFilter::compute(), core::pose::Pose::conformation(), protocols::scoring::Interface::distance(), distance_threshold_, protocols::scoring::Interface::is_interface(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pack::pack_rotamers(), core::pose::Pose::pdb_info(), repeats_, core::pose::Pose::residue(), scorefxn_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by report().

void protocols::simple_filters::AlaScan::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn)

Definition at line 73 of file AlaScan.cc.

References scorefxn_.

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

Member Data Documentation

bool protocols::simple_filters::AlaScan::chain1_

private

Definition at line 69 of file AlaScan.hh.

Referenced by chain1().

bool protocols::simple_filters::AlaScan::chain2_

private

Definition at line 69 of file AlaScan.hh.

Referenced by chain2().

core::Real protocols::simple_filters::AlaScan::distance_threshold_

private

Definition at line 71 of file AlaScan.hh.

Referenced by dist(), report(), and report_symmetry().

core::Size protocols::simple_filters::AlaScan::jump_

private

Definition at line 72 of file AlaScan.hh.

Referenced by jump().

bool protocols::simple_filters::AlaScan::repack_

private

Definition at line 75 of file AlaScan.hh.

Referenced by repack().

core::Size protocols::simple_filters::AlaScan::repeats_

private

Definition at line 70 of file AlaScan.hh.

Referenced by ddG_for_single_residue(), repeats(), report(), and report_symmetry().

core::scoring::ScoreFunctionOP protocols::simple_filters::AlaScan::scorefxn_

private

Definition at line 74 of file AlaScan.hh.

Referenced by AlaScan(), ddG_for_single_residue(), report(), report_symmetry(), and scorefxn().

bool protocols::simple_filters::AlaScan::symmetry_

private

Definition at line 73 of file AlaScan.hh.

Referenced by AlaScan().

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

• src/protocols/simple_filters/AlaScan.hh
• src/protocols/protein_interface_design/parse_filters.cc
• src/protocols/simple_filters/AlaScan.cc