#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_

Detailed Description

Definition at line 31 of file DdgFilter.hh.

Constructor & Destructor Documentation

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

Definition at line 54 of file DdgFilter.cc.

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`
	)

Definition at line 73 of file DdgFilter.cc.

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

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

virtual

Definition at line 103 of file DdgFilter.cc.

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.

Definition at line 215 of file DdgFilter.cc.

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

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

virtual

Implements protocols::filters::Filter.

Definition at line 105 of file DdgFilter.cc.

References DdgFilter().

Referenced by parse_def().

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

Definition at line 253 of file DdgFilter.cc.

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.

Definition at line 108 of file DdgFilter.cc.

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.

Definition at line 178 of file DdgFilter.cc.

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.

Definition at line 159 of file parse_filters.cc.

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

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

inline

Definition at line 58 of file DdgFilter.hh.

References relax_bound_.

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

inline

Definition at line 59 of file DdgFilter.hh.

References relax_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::relax_mover ( protocols::moves::MoverOP m)

Definition at line 310 of file DdgFilter.cc.

References relax_mover_.

protocols::moves::MoverOP protocols::simple_filters::DdgFilter::relax_mover ( ) const

Definition at line 315 of file DdgFilter.cc.

References relax_mover_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repack ( bool const repack)

Definition at line 113 of file DdgFilter.cc.

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

Definition at line 119 of file DdgFilter.cc.

References repack_.

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

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

inline

Definition at line 56 of file DdgFilter.hh.

References repack_bound_.

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

inline

Definition at line 57 of file DdgFilter.hh.

References repack_bound_.

Referenced by compute().

void protocols::simple_filters::DdgFilter::repeats ( core::Size const repeats)

Definition at line 247 of file DdgFilter.cc.

References repeats(), and repeats_.

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

Definition at line 241 of file DdgFilter.cc.

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.

Definition at line 229 of file DdgFilter.cc.

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.

Definition at line 235 of file DdgFilter.cc.

References compute().

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

inline

Definition at line 61 of file DdgFilter.hh.

References task_factory(), and task_factory_.

Referenced by task_factory().

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

inline

Definition at line 62 of file DdgFilter.hh.

References task_factory_.

Referenced by compute().

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

inline

Definition at line 63 of file DdgFilter.hh.

References use_custom_task_.

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

inline

Definition at line 64 of file DdgFilter.hh.

References use_custom_task_.

Referenced by compute().

Member Data Documentation

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

private

Definition at line 87 of file DdgFilter.hh.

Referenced by compute(), and parse_def().

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

private

Definition at line 80 of file DdgFilter.hh.

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.

Definition at line 41 of file DdgFilter.hh.

Referenced by parse_def().

bool protocols::simple_filters::DdgFilter::pb_enabled_

private

is PB enabled?

Definition at line 94 of file DdgFilter.hh.

Referenced by DdgFilter().

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

private

Definition at line 82 of file DdgFilter.hh.

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::relax_bound_

private

Definition at line 86 of file DdgFilter.hh.

Referenced by parse_def(), and relax_bound().

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

private

Definition at line 91 of file DdgFilter.hh.

Referenced by relax_mover().

bool protocols::simple_filters::DdgFilter::repack_

private

Definition at line 90 of file DdgFilter.hh.

Referenced by repack().

bool protocols::simple_filters::DdgFilter::repack_bound_

private

Definition at line 85 of file DdgFilter.hh.

Referenced by parse_def(), and repack_bound().

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

private

Definition at line 88 of file DdgFilter.hh.

Referenced by compute(), and repeats().

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

private

Definition at line 81 of file DdgFilter.hh.

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

bool protocols::simple_filters::DdgFilter::symmetry_

private

Definition at line 89 of file DdgFilter.hh.

Referenced by compute(), and parse_def().

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

private

Definition at line 83 of file DdgFilter.hh.

Referenced by task_factory().

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

private

translation distance in A

Definition at line 97 of file DdgFilter.hh.

Referenced by compute(), and parse_def().

bool protocols::simple_filters::DdgFilter::use_custom_task_

private

Definition at line 84 of file DdgFilter.hh.

Referenced by use_custom_task().

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

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation