#include <ddG.hh>

Public Types
typedef core::Real	Real

typedef core::scoring::ScoreType	ScoreType

typedef core::pose::Pose	Pose

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	ddG ()

	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump=1)

	ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump, utility::vector1< core::Size > const &chain_ids)

virtual void	apply (Pose &pose)

void	calculate (Pose const &pose_in)
	compute the energy of the repacked complex in the bound and unbound states More...

void	report_ddG (std::ostream &out) const

Real	sum_ddG () const

core::Size	rb_jump () const

void	rb_jump (core::Size j)

core::Size	repeats () const

void	repeats (core::Size repeats)

core::Real	translate_by () const

void	translate_by (core::Real translate_by)

virtual	~ddG ()

protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

void	parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

protocols::moves::MoverOP	relax_mover () const

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

protocols::filters::FilterOP	filter () const

void	filter (protocols::filters::FilterOP f)

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	repack_bound (bool rpb)

bool	repack_bound () const

void	relax_bound (bool rlb)

bool	relax_bound () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

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

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	unbind (Pose &pose) const
	Helper method to appropriately form unbound complex. More...

void	setup_task (Pose const &pose)

void	fill_energy_vector (Pose const &pose, std::map< ScoreType, Real > &energy_map)

void	fill_per_residue_energy_vector (Pose const &pose, std::map< Size, Real > &energy_map)

Private Attributes
std::map< ScoreType, Real >	bound_energies_

std::map< ScoreType, Real >	unbound_energies_

std::map< Size, Real >	bound_per_residue_energies_

std::map< Size, Real >	unbound_per_residue_energies_

Real	bound_total_energy_

Real	unbound_total_energy_

Size	repeats_

core::scoring::ScoreFunctionOP	scorefxn_

core::Size	rb_jump_

utility::vector1< core::Size >	chain_ids_

bool	per_residue_ddg_

bool	repack_

protocols::moves::MoverOP	relax_mover_

protocols::filters::FilterOP	filter_

core::pack::task::TaskFactoryOP	task_factory_

core::pack::task::PackerTaskOP	task_

bool	use_custom_task_

bool	repack_bound_

bool	relax_bound_

core::scoring::methods::PBLifetimeCacheOP	pb_cached_data_
	info carrier for poisson-boltzmann potential energy computation More...

bool	pb_enabled_
	true when PB potential is part of scorefxn More...

core::Real	translate_by_
	distance in A to separate moledules More...

Additional Inherited Members
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

typedef core::pose::Pose protocols::simple_moves::ddG::Pose

typedef core::Real protocols::simple_moves::ddG::Real

typedef core::scoring::ScoreType protocols::simple_moves::ddG::ScoreType

Constructor & Destructor Documentation

protocols::simple_moves::ddG::ddG ( )

References bound_energies_, bound_per_residue_energies_, unbound_energies_, and unbound_per_residue_energies_.

Referenced by clone(), and fresh_instance().

protocols::simple_moves::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump = `1`
	)

References bound_energies_, bound_per_residue_energies_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_moves::TR, unbound_energies_, and unbound_per_residue_energies_.

protocols::simple_moves::ddG::ddG	(	core::scoring::ScoreFunctionCOP	scorefxn_in,
		core::Size const	jump,
		utility::vector1< core::Size > const &	chain_ids
	)

References bound_energies_, bound_per_residue_energies_, chain_ids_, core::scoring::PB_elec, pb_enabled_, scorefxn_, protocols::simple_moves::TR, unbound_energies_, and unbound_per_residue_energies_.

protocols::simple_moves::ddG::~ddG ( )

virtual

Member Function Documentation

void protocols::simple_moves::ddG::apply ( Pose & pose )

virtual

void protocols::simple_moves::ddG::calculate ( pose::Pose const & pose_original )

compute the energy of the repacked complex in the bound and unbound states

Parameters

pose_in The base pose.

Returns: Nothing, but the base pose's cache be augmented with extra cached data if the scorefunction contains non-zero PB_elec term.

References protocols::moves::Mover::apply(), bound_energies_, bound_per_residue_energies_, fill_energy_vector(), fill_per_residue_energy_vector(), core::pose::symmetry::is_symmetric(), pb_cached_data_, pb_enabled_, per_residue_ddg_, relax_bound(), relax_mover(), repack_, repack_bound(), runtime_assert, scorefxn_, setup_task(), core::scoring::symmetry::symmetrize_scorefunction(), task_, unbind(), unbound_energies_, and unbound_per_residue_energies_.

Referenced by apply(), protocols::simple_filters::DdgFilter::compute(), ddG_cycles(), protocols::simple_filters::TaskAwareAlaScan::ddG_for_single_residue(), and protocols::simple_filters::TaskAwareAlaScan::report().

protocols::moves::MoverOP protocols::simple_moves::ddG::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References ddG().

void protocols::simple_moves::ddG::fill_energy_vector	(	pose::Pose const &	pose,
		std::map< ScoreType, Real > &	energy_map
	)

private

a private function for storing energy values

References core::pose::Pose::energies(), filter_, n_score_types, pro_close, protocols::filters::Filter::report(), protocols::filters::Filter::report_sm(), scorefxn_, core::scoring::Energies::total_energies(), core::scoring::total_score, and protocols::simple_moves::TR.

Referenced by calculate().

void protocols::simple_moves::ddG::fill_per_residue_energy_vector	(	pose::Pose const &	pose,
		std::map< Size, Real > &	energy_map
	)

private

References core::pose::Pose::energies(), filter_, n_score_types, pro_close, core::scoring::Energies::residue_total_energies(), scorefxn_, core::pose::Pose::total_residue(), and utility_exit_with_message.

Referenced by calculate().

protocols::filters::FilterOP protocols::simple_moves::ddG::filter ( ) const

References filter_.

Referenced by protocols::simple_filters::DdgFilter::compute(), and parse_my_tag().

void protocols::simple_moves::ddG::filter ( protocols::filters::FilterOP f )

References filter_.

protocols::moves::MoverOP protocols::simple_moves::ddG::fresh_instance ( ) const

inlinevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ddG().

std::string protocols::simple_moves::ddG::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

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

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References chain_ids_, core::scoring::ScoreFunction::clone(), filter(), core::pose::get_chain_id_from_chain(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound_, relax_mover(), repack_, repack_bound_, repeats_, scorefxn_, utility::string_split(), task_factory(), protocols::simple_moves::TR, translate_by_, and use_custom_task().