#include <DdGScan.hh>

Inheritance diagram for protocols::simple_filters::DdGScan:

Public Member Functions
	DdGScan ()
	default constructor More...

	DdGScan (core::pack::task::TaskFactoryOP task_factory, core::Size const repeats, core::scoring::ScoreFunctionCOP scorefxn, bool report_diffs, bool write2pdb)
	constructor with arguments More...

	DdGScan (DdGScan const &rval)
	copy constructor More...

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

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

virtual	~DdGScan ()
	destructor More...

void	initialize ()

virtual std::string	name () const

void	task_factory (core::pack::task::TaskFactoryOP task_factory)

void	repeats (core::Size const r)

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

void	report_diffs (bool const report_diffs)

void	write2pdb (bool const write)

void	ddG_mover (protocols::simple_moves::ddGOP const ddG_mover_op)

core::pack::task::TaskFactoryOP	task_factory () const

core::Size	repeats () const

bool	report_diffs () const

bool	write2pdb () const

protocols::simple_moves::ddGOP	ddG_mover () const

virtual bool	apply (core::pose::Pose const &) const
	Dummy Filter apply function. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &movers, core::pose::Pose const &)
	parse xml More...

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

core::Real	ddG_for_single_residue (core::pose::Pose const &const_pose, core::Size const resi, core::pack::task::PackerTaskOP const general_task, core::pose::Pose &pose_to_mutate) const
	Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0) More...

void	write_to_pdb (core::pose::Pose const &pose, core::Size const &residue, core::Size const &output_resi, std::string const &residue_name, core::Real const &ddG) const

virtual void	report (std::ostream &out, core::pose::Pose const &pose) const
	Implementation of virtual report function. More...

utility::vector1< ddG_data_tuple >	calculate (std::ostream &out, core::pose::Pose const &pose) const
	calculate and report the per-residue ddGs More...

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

	Filter (std::string const &)

	Filter (Filter const &)

virtual	~Filter ()

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

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)

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_

core::Size	repeats_

core::scoring::ScoreFunctionOP	scorefxn_

bool	report_diffs_

bool	write2pdb_

protocols::simple_moves::ddGOP	ddG_mover_

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

Constructor & Destructor Documentation

protocols::simple_filters::DdGScan::DdGScan ( )

default constructor

References initialize().

Referenced by clone(), and fresh_instance().

protocols::simple_filters::DdGScan::DdGScan	(	core::pack::task::TaskFactoryOP	task_factory,
		core::Size const	repeats,
		core::scoring::ScoreFunctionCOP	scorefxn,
		bool	report_diffs,
		bool	write2pdb
	)

constructor with arguments

References initialize().

protocols::simple_filters::DdGScan::DdGScan ( DdGScan const & rval )

copy constructor

protocols::simple_filters::DdGScan::~DdGScan ( )

virtual

destructor

Member Function Documentation

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

virtual

Dummy Filter apply function.

Implements protocols::filters::Filter.

utility::vector1< ddG_data_tuple > protocols::simple_filters::DdGScan::calculate	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

calculate and report the per-residue ddGs

References core::pack::task::TaskFactory::create_packer_task(), ddG_for_single_residue(), core::chemical::element::F, core::conformation::Residue::is_protein(), core::pose::Pose::n_residue(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), report_diffs(), core::pose::Pose::residue(), task_factory_, protocols::simple_filters::TR(), write2pdb(), and write_to_pdb().

Referenced by report().

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

virtual

Implements protocols::filters::Filter.

References DdGScan().

Referenced by parse_def().

core::Real protocols::simple_filters::DdGScan::ddG_for_single_residue	(	core::pose::Pose const &	const_pose,
		core::Size const	resi,
		core::pack::task::PackerTaskOP const	general_task,
		core::pose::Pose &	pose_to_mutate
	)		const

Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0)

References protocols::jd2::current_output_name(), ddG_mover_, core::pose::symmetry::is_symmetric(), core::conformation::Residue::name3(), core::pack::pack_rotamers(), repeats(), core::pose::Pose::residue(), scorefxn_, core::scoring::symmetry::symmetrize_scorefunction(), core::pose::Pose::total_residue(), and protocols::simple_filters::TR().

Referenced by calculate().

void protocols::simple_filters::DdGScan::ddG_mover ( protocols::simple_moves::ddGOP const ddG_mover_op )

References ddG_mover_.

protocols::simple_moves::ddGOP protocols::simple_filters::DdGScan::ddG_mover ( ) const

References ddG_mover_.

Referenced by initialize(), and parse_my_tag().

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

virtual

Implements protocols::filters::Filter.

References DdGScan().

void protocols::simple_filters::DdGScan::initialize ( )

References ddG_mover().

Referenced by DdGScan().

virtual std::string protocols::simple_filters::DdGScan::name ( ) const

inlinevirtual

Reimplemented from protocols::filters::Filter.

Referenced by write_to_pdb().

void protocols::simple_filters::DdGScan::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 clone(), protocols::elscripts::parse_scoredef(), protocols::elscripts::parse_taskdef(), repeats(), report_diffs(), scorefxn_, task_factory(), and write2pdb().

void protocols::simple_filters::DdGScan::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &
	)

virtual

parse xml

Reimplemented from protocols::filters::Filter.

References ddG_mover(), protocols::rosetta_scripts::parse_mover(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), repeats(), report_diffs(), scorefxn_, task_factory(), and write2pdb().

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

References repeats_.

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

References repeats_.

Referenced by ddG_for_single_residue(), parse_def(), and parse_my_tag().

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

virtual

Implementation of virtual report function.

Calls report function with return value

Reimplemented from protocols::filters::Filter.

References calculate().

void protocols::simple_filters::DdGScan::report_diffs ( bool const report_diffs )

References report_diffs(), and report_diffs_.

bool protocols::simple_filters::DdGScan::report_diffs ( ) const

References report_diffs_.

Referenced by calculate(), parse_def(), parse_my_tag(), and report_diffs().

void protocols::simple_filters::DdGScan::scorefxn ( core::scoring::ScoreFunctionOP const scorefxn )

References scorefxn_.

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

References task_factory(), and task_factory_.

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

References task_factory_.

Referenced by parse_def(), parse_my_tag(), and task_factory().

void protocols::simple_filters::DdGScan::write2pdb ( bool const write )

References write2pdb_.

bool protocols::simple_filters::DdGScan::write2pdb ( ) const

References write2pdb_.

Referenced by calculate(), parse_def(), and parse_my_tag().

void protocols::simple_filters::DdGScan::write_to_pdb	(	core::pose::Pose const &	pose,
		core::Size const &	residue,
		core::Size const &	output_resi,
		std::string const &	residue_name,
		core::Real const &	ddG
	)		const