protocols::simple_filters::DdgFilter Class Reference

#include <DdgFilter.hh>

Inheritance diagram for protocols::simple_filters::DdgFilter:

Collaboration diagram for protocols::simple_filters::DdgFilter:

Public Member Functions
	DdgFilter ()
	DdgFilter (core::Real const ddg_threshold, core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1, core::Size const repeats=1, bool const symmetry=false)
bool	apply (core::pose::Pose const &pose) const
	Returns true if the given pose passes the filter, false otherwise. More...
filters::FilterOP	clone () const
filters::FilterOP	fresh_instance () const
void	repack (bool const repack)
bool	repack () const
void	repeats (core::Size const repeats)
void	repack_bound (bool rpb)
bool	repack_bound () const
void	relax_bound (bool rlb)
bool	relax_bound () const
core::Size	repeats () const
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
core::pack::task::TaskFactoryOP	task_factory () const
void	use_custom_task (bool uct)
bool	use_custom_task () const
void	report (std::ostream &out, core::pose::Pose const &pose) const
core::Real	report_sm (core::pose::Pose const &pose) const
	used to report filter internals through a score or silent file More...
core::Real	compute (core::pose::Pose const &pose) const
virtual	~DdgFilter ()
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 &)
void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
void	relax_mover (protocols::moves::MoverOP m)
protocols::moves::MoverOP	relax_mover () 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 std::string	name () const

Static Public Attributes
static const core::Real	DEFAULT_TRANSLATION_DISTANCE = 100.0

Private Member Functions
void	initPB ()

Private Attributes
core::Real	ddg_threshold_
core::scoring::ScoreFunctionOP	scorefxn_
core::Size	rb_jump_
core::pack::task::TaskFactoryOP	task_factory_
bool	use_custom_task_
bool	repack_bound_
bool	relax_bound_
utility::vector1< core::Size >	chain_ids_
core::Size	repeats_
bool	symmetry_
bool	repack_
protocols::moves::MoverOP	relax_mover_
bool	pb_enabled_
	is PB enabled? More...
core::Real	translate_by_
	translation distance in A More...

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

Constructor & Destructor Documentation

protocols::simple_filters::DdgFilter::DdgFilter

(

)

References protocols::filters::Filter::scorename_.

Referenced by clone(), and fresh_instance().

protocols::simple_filters::DdgFilter::DdgFilter	(	core::Real const	ddg_threshold,
		core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	rb_jump = 1,
		core::Size const	repeats = 1,
		bool const	symmetry = false
	)

References core::scoring::PB_elec, pb_enabled_, scorefxn_, and protocols::simple_filters::TR().

protocols::simple_filters::DdgFilter::~DdgFilter ( )

virtual

Member Function Documentation

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

virtual

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

Implements protocols::filters::Filter.

References compute(), ddg_threshold_, and protocols::simple_filters::TR().

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

virtual

Implements protocols::filters::Filter.

References DdgFilter().

Referenced by parse_def().

core::Real protocols::simple_filters::DdgFilter::compute

(

core::pose::Pose const &

pose)

const

References protocols::simple_moves::ddG::calculate(), chain_ids_, protocols::simple_filters::ScoreTypeFilter::compute(), core::pose::get_jump_id_from_chain_id(), rb_jump_, relax_bound(), protocols::simple_moves::ddG::relax_bound(), relax_mover(), protocols::simple_moves::ddG::relax_mover(), repack(), repack_bound(), protocols::simple_moves::ddG::repack_bound(), repeats(), repeats_, protocols::simple_moves::ddG::report_ddG(), scorefxn_, protocols::simple_moves::ddG::sum_ddG(), symmetry_, task_factory(), protocols::simple_moves::ddG::task_factory(), core::scoring::total_score, protocols::simple_filters::TR(), protocols::swa::translate(), translate_by_, use_custom_task(), and protocols::simple_moves::ddG::use_custom_task().

Referenced by apply(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::simple_filters::AlaScan::report(), report(), report_sm(), and protocols::simple_filters::AlaScan::report_symmetry().

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

virtual

Implements protocols::filters::Filter.

References DdgFilter().

void protocols::simple_filters::DdgFilter::initPB ( )

private

void protocols::simple_filters::DdgFilter::parse_def ( utility::lua::LuaObject const &  def, utility::lua::LuaObject const &  score_fxns, utility::lua::LuaObject const &  tasks  )

virtual

Reimplemented from protocols::filters::Filter.

References chain_ids_, clone(), ddg_threshold_, DEFAULT_TRANSLATION_DISTANCE, core::sequence::end, protocols::elscripts::parse_scoredef(), rb_jump_, relax_bound_, repack(), repack_bound_, repeats(), scorefxn_, protocols::filters::Filter::scorename_, symmetry_, protocols::simple_filters::TR(), and translate_by_.

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

virtual

Reimplemented from protocols::filters::Filter.

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

void protocols::simple_filters::DdgFilter::relax_bound ( bool  rlb)

inline

References relax_bound_.

bool protocols::simple_filters::DdgFilter::relax_bound ( ) const

inline

References relax_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::relax_mover

(

protocols::moves::MoverOP

m)

References relax_mover_.

protocols::moves::MoverOP protocols::simple_filters::DdgFilter::relax_mover

(

)

const

References relax_mover_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repack

(

bool const

repack)

References repack(), and repack_.

Referenced by protocols::simple_filters::RotamerBoltzmannWeight::compute_modified_ddG(), protocols::simple_filters::AlaScan::ddG_for_single_residue(), and protocols::simple_filters::RotamerBoltzmannWeight::first_pass_ala_scan().

bool protocols::simple_filters::DdgFilter::repack

(

)

const

References repack_.

Referenced by compute(), parse_def(), and repack().

void protocols::simple_filters::DdgFilter::repack_bound ( bool  rpb)

inline

References repack_bound_.

bool protocols::simple_filters::DdgFilter::repack_bound ( ) const

inline

References repack_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repeats

(

core::Size const

repeats)

References repeats(), and repeats_.

core::Size protocols::simple_filters::DdgFilter::repeats

(

)

const

References repeats_.

Referenced by compute(), parse_def(), and repeats().

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

virtual

Reimplemented from protocols::filters::Filter.

References compute().

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

virtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute().

void protocols::simple_filters::DdgFilter::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

inline

References task_factory(), and task_factory_.

Referenced by task_factory().

core::pack::task::TaskFactoryOP protocols::simple_filters::DdgFilter::task_factory ( ) const

inline

References task_factory_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::use_custom_task ( bool  uct)

inline

References use_custom_task_.

bool protocols::simple_filters::DdgFilter::use_custom_task ( ) const

inline

References use_custom_task_.

Referenced by compute().

Member Data Documentation

utility::vector1<core::Size> protocols::simple_filters::DdgFilter::chain_ids_

private

Referenced by compute(), and parse_def().

core::Real protocols::simple_filters::DdgFilter::ddg_threshold_

private

Referenced by apply(), and parse_def().

const core::Real protocols::simple_filters::DdgFilter::DEFAULT_TRANSLATION_DISTANCE = 100.0

static

Distance in A to separate the molecules away from bound-state. NOTES by Sachko Honda: This value used to be hard coded to 1000 for unbound poses, whereas the default 100 was used for bounded. The choice of value 1000 was arbitrary by the original author. The value is now reduced to 100 in order to help the PDE solver (APBS) from blowing up, by default, but can be a user-defined value via RosettaScript option or command-line option.

Referenced by parse_def().

bool protocols::simple_filters::DdgFilter::pb_enabled_

private

is PB enabled?

Referenced by DdgFilter().

core::Size protocols::simple_filters::DdgFilter::rb_jump_

private

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::relax_bound_

private

Referenced by parse_def(), and relax_bound().

protocols::moves::MoverOP protocols::simple_filters::DdgFilter::relax_mover_

private

Referenced by relax_mover().

bool protocols::simple_filters::DdgFilter::repack_

private

Referenced by repack().

bool protocols::simple_filters::DdgFilter::repack_bound_

private

Referenced by parse_def(), and repack_bound().

core::Size protocols::simple_filters::DdgFilter::repeats_

private

Referenced by compute(), and repeats().

core::scoring::ScoreFunctionOP protocols::simple_filters::DdgFilter::scorefxn_

private

Referenced by compute(), DdgFilter(), and parse_def().

bool protocols::simple_filters::DdgFilter::symmetry_

private

Referenced by compute(), and parse_def().

core::pack::task::TaskFactoryOP protocols::simple_filters::DdgFilter::task_factory_

private

Referenced by task_factory().

core::Real protocols::simple_filters::DdgFilter::translate_by_

private

translation distance in A

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::use_custom_task_

private

Referenced by use_custom_task().

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

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