this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction. More...

#include <ConformerSwitchMover.hh>

Public Member Functions
	ConformerSwitchMover ()

	ConformerSwitchMover (protocols::docking::DockingEnsembleOP ensemble, bool random_conformer=false)

virtual void	apply (core::pose::Pose &pose)

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

void	switch_conformer (core::pose::Pose &pose, core::Size conf_num)

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

void	set_temperature (core::Real temp_in)

void	set_random_confomer (bool rand)

core::Real	get_temperature () const

bool	use_random_conformer () 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)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

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

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...

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

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	GenerateProbTable (core::pose::Pose &pose)

Private Attributes
bool	random_conformer_

core::Real	temperature_

utility::vector1< core::Real >	prob_table_

protocols::docking::DockingEnsembleOP	ensemble_

protocols::docking::DockingLowResFilterOP	lowres_filter_

Additional Inherited Members
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

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...

Detailed Description

this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

Constructor & Destructor Documentation

protocols::docking::ConformerSwitchMover::ConformerSwitchMover ( )

References protocols::moves::Mover::type().

protocols::docking::ConformerSwitchMover::ConformerSwitchMover	(	protocols::docking::DockingEnsembleOP	ensemble,
		bool	random_conformer = `false`
	)

References ensemble_, and lowres_filter_.

Member Function Documentation

void protocols::docking::ConformerSwitchMover::apply ( core::pose::Pose & pose )

virtual

Implements protocols::moves::Mover.

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, core::pose::Pose::data(), ensemble_, GenerateProbTable(), basic::datacache::BasicDataCache::get_raw_ptr(), basic::datacache::BasicDataCache::has(), lowres_filter_, basic::datacache::CacheableStringFloatMap::map(), prob_table_, random_conformer_, numeric::random::RandomGenerator::random_range(), protocols::RG, basic::datacache::BasicDataCache::set(), switch_conformer(), protocols::TR, and numeric::random::RandomGenerator::uniform().

void protocols::docking::ConformerSwitchMover::GenerateProbTable ( core::pose::Pose & pose )

private

References ensemble_, prob_table_, switch_conformer(), and temperature_.

Referenced by apply().

std::string protocols::docking::ConformerSwitchMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

References protocols::docking::ConformerSwitchMoverCreator::mover_name().

core::Real protocols::docking::ConformerSwitchMover::get_temperature ( ) const

inline

References temperature_.

Referenced by show().

void protocols::docking::ConformerSwitchMover::set_random_confomer ( bool rand )

inline

References random_conformer_.

void protocols::docking::ConformerSwitchMover::set_temperature ( core::Real temp_in )

References temperature_.

void protocols::docking::ConformerSwitchMover::show ( std::ostream & output = std::cout ) const

virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References get_temperature(), protocols::moves::Mover::show(), and use_random_conformer().

Referenced by protocols::docking::operator<<().

void protocols::docking::ConformerSwitchMover::switch_conformer	(	core::pose::Pose &	pose,
		core::Size	conf_num
	)

References core::conformation::Residue::atom_index(), core::id::BOGUS_ATOM_ID, protocols::scoring::Interface::calculate(), core::pose::Pose::copy_segment(), ensemble_, core::pose::initialize_atomid_map(), core::pose::Pose::residue(), and core::scoring::superimpose_pose().

Referenced by apply(), and GenerateProbTable().

bool protocols::docking::ConformerSwitchMover::use_random_conformer ( ) const

inline

References random_conformer_.

Referenced by show().

Member Data Documentation

protocols::docking::DockingEnsembleOP protocols::docking::ConformerSwitchMover::ensemble_

private

Referenced by apply(), ConformerSwitchMover(), GenerateProbTable(), and switch_conformer().

protocols::docking::DockingLowResFilterOP protocols::docking::ConformerSwitchMover::lowres_filter_

private

Referenced by apply(), and ConformerSwitchMover().

utility::vector1< core::Real > protocols::docking::ConformerSwitchMover::prob_table_

private

Referenced by apply(), and GenerateProbTable().

bool protocols::docking::ConformerSwitchMover::random_conformer_

private

Referenced by apply(), set_random_confomer(), and use_random_conformer().

core::Real protocols::docking::ConformerSwitchMover::temperature_

private

Referenced by GenerateProbTable(), get_temperature(), and set_temperature().

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

src/protocols/docking/ConformerSwitchMover.hh
src/protocols/docking/ConformerSwitchMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation