#include <SymDockProtocol.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockProtocol:

Collaboration diagram for protocols::symmetric_docking::SymDockProtocol:

Public Types
typedef core::conformation::symmetry::SymmetricConformation	SymmetricConformation

typedef core::conformation::symmetry::SymmetryInfo	SymmetryInfo

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

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
	SymDockProtocol ()

	SymDockProtocol (bool const fullatom, bool const local_refine, bool const view=false)

	SymDockProtocol (bool const fullatom, bool const local_refine, bool const view, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)

virtual	~SymDockProtocol ()

void	set_default ()
	setup that is called from constructor More...

void	register_options ()

void	set_dock_rtmin (bool dock_rtmin_in)
	setter More...

void	set_sc_min (bool sc_min_in)

void	set_max_repeats (Size const max_repeats_in)

void	set_dock_ppk (bool dock_ppk_in)

void	set_fullatom (bool const fullatom_in)

void	set_local_refine (bool const local_refine_in)

void	set_view (bool view_in)

void	set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_score_low_in)

void	set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in)

void	set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_score_high_in, core::scoring::ScoreFunctionOP docking_score_pack_in)

bool	docking_lowres_filter (core::pose::Pose &pose)

bool	docking_highres_filter (core::pose::Pose &pose)

core::Real	calc_interaction_energy (core::pose::Pose &pose)

core::Real	calc_rms (core::pose::Pose &pose)

void	recover_sidechains (core::pose::Pose &pose, const core::pose::Pose &native_pose)
	recovers the side-chains from the native-pose More...

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

void	design (bool const des)

bool	design () const

void	hurry (bool const hurry)

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

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

void	score_only (core::pose::Pose &pose)

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

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

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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

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 void	parse_my_tag (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	classic_mcm_protocol (core::pose::Pose &pose, core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo, core::Size num_cycles, core::Size repack_every_Nth) const

protocols::moves::MoverOP	make_dockmcm_mover (core::pose::Pose const &pose, protocols::moves::MoverOP repack_mover, protocols::moves::MoverOP rigbod_mover, core::kinematics::MoveMapOP movemap, core::scoring::symmetry::SymmetricScoreFunctionOP scorefxn, protocols::moves::MonteCarloOP monteCarlo) const

Private Attributes
bool	fullatom_
	information about the mode More...

bool	local_refine_

bool	rtmin_

bool	sc_min_

Size	max_repeats_

bool	dock_ppk_

utility::vector1< core::Size >	movable_jumps_
	the jump number across which to do rigid_body transformations More...

bool	autofoldtree_
	should docking change the foldtree? More...

bool	view_
	whether or not to initialize the viewer (for opengl) More...

bool	design_

bool	passed_lowres_filter_

bool	passed_highres_filter_

bool	hurry_

std::map< std::string, core::Real >	score_map_

core::scoring::ScoreFunctionOP	docking_score_low_

core::scoring::ScoreFunctionOP	docking_score_high_

core::scoring::ScoreFunctionOP	docking_score_high_min_

core::scoring::ScoreFunctionOP	docking_score_pack_

moves::MonteCarloOP	mc_

protocols::symmetric_docking::SymDockingLowResOP	docking_low_

protocols::symmetric_docking::SymDockingHiResOP	docking_high_

core::pack::task::TaskFactoryOP	init_task_factory_

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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::conformation::symmetry::SymmetricConformation protocols::symmetric_docking::SymDockProtocol::SymmetricConformation

typedef core::conformation::symmetry::SymmetryInfo protocols::symmetric_docking::SymDockProtocol::SymmetryInfo

Constructor & Destructor Documentation

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol ( )

References register_options(), and set_default().

Referenced by clone().

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol	(	bool const	fullatom,
		bool const	local_refine,
		bool const	view = `false`
	)

References register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

protocols::symmetric_docking::SymDockProtocol::SymDockProtocol	(	bool const	fullatom,
		bool const	local_refine,
		bool const	view,
		core::scoring::ScoreFunctionOP	docking_score_low,
		core::scoring::ScoreFunctionOP	docking_score_high
	)

References docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, register_options(), set_default(), set_fullatom(), set_local_refine(), and set_view().

protocols::symmetric_docking::SymDockProtocol::~SymDockProtocol ( )

virtual

Member Function Documentation

void protocols::symmetric_docking::SymDockProtocol::apply ( core::pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ConstraintSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), core::scoring::atom_pair_constraint, calc_interaction_energy(), calc_rms(), core::chemical::CENTROID, core::pose::Pose::conformation(), protocols::nonlocal::current_job(), core::pose::Pose::data(), core::pack::interaction_graph::debug, design_, docking_high_, docking_highres_filter(), docking_low_, docking_lowres_filter(), docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, core::chemical::FA_STANDARD, fullatom_, protocols::moves::Mover::get_input_pose(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), core::scoring::getScoreFunction(), hurry_, init_task_factory_, core::pose::Pose::is_fullatom(), local_refine_, protocols::jd2::ScoreMap::nonzero_energies(), passed_highres_filter_, passed_lowres_filter_, recover_sidechains(), protocols::relax::relax_pose(), core::scoring::rms, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, score_only(), set_highres_scorefxn(), protocols::moves::Mover::set_input_pose(), set_lowres_scorefxn(), protocols::medal::to_centroid(), and protocols::symmetric_docking::TR().

core::Real protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy ( core::pose::Pose & pose)

References core::pose::Pose::conformation(), docking_score_high_, docking_score_low_, fullatom_, core::pose::symmetry::is_symmetric(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by apply().

core::Real protocols::symmetric_docking::SymDockProtocol::calc_rms ( core::pose::Pose & pose)

References core::scoring::CA_rmsd_symmetric(), core::pose::Pose::conformation(), protocols::moves::Mover::get_native_pose(), core::scoring::is_protein_CA(), core::pose::symmetry::is_symmetric(), core::scoring::rmsd_with_super_subset(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

Referenced by apply(), and score_only().

void protocols::symmetric_docking::SymDockProtocol::classic_mcm_protocol	(	core::pose::Pose &	pose,
		core::scoring::symmetry::SymmetricScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo,
		core::Size	num_cycles,
		core::Size	repack_every_Nth
	)		const

private

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

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 docking_score_high_, docking_score_low_, fullatom_, local_refine_, SymDockProtocol(), and view_.

void protocols::symmetric_docking::SymDockProtocol::design ( bool const des)

References design_.

bool protocols::symmetric_docking::SymDockProtocol::design ( ) const

References design_.

Referenced by set_default().

bool protocols::symmetric_docking::SymDockProtocol::docking_highres_filter ( core::pose::Pose & pose)

References core::pose::Pose::energies(), score_map_, core::scoring::Energies::total_energy(), and protocols::symmetric_docking::TR().

Referenced by apply().

bool protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter ( core::pose::Pose & pose)

References core::scoring::atom_pair_constraint, core::pose::Pose::energies(), core::scoring::interchain_contact, core::scoring::interchain_vdw, core::scoring::saxs::ref_spectrum, core::pose::setPoseExtraScores(), core::scoring::Energies::total_energies(), and protocols::symmetric_docking::TR().

Referenced by apply().

std::string protocols::symmetric_docking::SymDockProtocol::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::symmetric_docking::SymDockProtocol::hurry ( bool const hurry)

References hurry_.

Referenced by set_default().

protocols::moves::MoverOP protocols::symmetric_docking::SymDockProtocol::make_dockmcm_mover	(	core::pose::Pose const &	pose,
		protocols::moves::MoverOP	repack_mover,
		protocols::moves::MoverOP	rigbod_mover,
		core::kinematics::MoveMapOP	movemap,
		core::scoring::symmetry::SymmetricScoreFunctionOP	scorefxn,
		protocols::moves::MonteCarloOP	monteCarlo
	)		const

private

void protocols::symmetric_docking::SymDockProtocol::recover_sidechains	(	core::pose::Pose &	pose,
		const core::pose::Pose &	native_pose
	)

recovers the side-chains from the native-pose

References protocols::simple_moves::ReturnSidechainMover::apply(), docking_score_pack_, core::pack::task::TaskFactory::push_back(), rtmin_, and protocols::symmetric_docking::TR().

Referenced by apply().

void protocols::symmetric_docking::SymDockProtocol::register_options ( )

References core::import_pose::pose_from_pdb(), set_dock_ppk(), set_dock_rtmin(), set_fullatom(), set_local_refine(), set_max_repeats(), protocols::moves::Mover::set_native_pose(), and set_sc_min().

Referenced by SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::score_only ( core::pose::Pose & pose)

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ScoreMover::apply(), calc_rms(), core::chemical::CENTROID, docking_score_high_, docking_score_low_, fullatom_, protocols::simple_moves::ScoreMover::insert_rms(), and protocols::medal::to_centroid().

Referenced by apply().

void protocols::symmetric_docking::SymDockProtocol::set_default ( )

setup that is called from constructor

References core::scoring::electron_density::add_dens_scores_from_cmdline_to_scorefxn(), core::scoring::ScoreFunctionFactory::create_score_function(), design(), dock_ppk_, docking_score_high_, docking_score_high_min_, docking_score_low_, docking_score_pack_, hurry(), passed_highres_filter_, passed_lowres_filter_, and set_local_refine().

Referenced by SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::set_dock_ppk ( bool dock_ppk_in)

References dock_ppk_.

Referenced by register_options().

void protocols::symmetric_docking::SymDockProtocol::set_dock_rtmin ( bool dock_rtmin_in)

setter

References rtmin_.

Referenced by register_options().

void protocols::symmetric_docking::SymDockProtocol::set_fullatom ( bool const fullatom_in)

References fullatom_, and passed_highres_filter_.

Referenced by register_options(), set_local_refine(), and SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn ( core::scoring::ScoreFunctionOP docking_score_high_in)

References docking_high_, docking_score_high_, and docking_score_high_min_.

Referenced by apply().

void protocols::symmetric_docking::SymDockProtocol::set_highres_scorefxn	(	core::scoring::ScoreFunctionOP	docking_score_high_in,
		core::scoring::ScoreFunctionOP	docking_score_pack_in
	)

References docking_score_high_, docking_score_high_min_, and docking_score_pack_.

void protocols::symmetric_docking::SymDockProtocol::set_local_refine ( bool const local_refine_in)

References local_refine_, passed_lowres_filter_, and set_fullatom().

Referenced by register_options(), set_default(), and SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP docking_score_low_in)

References docking_low_, and docking_score_low_.

Referenced by apply().

void protocols::symmetric_docking::SymDockProtocol::set_max_repeats ( Size const max_repeats_in)

References max_repeats_.

Referenced by register_options().

void protocols::symmetric_docking::SymDockProtocol::set_sc_min ( bool sc_min_in)

References sc_min_.

Referenced by register_options().

void protocols::symmetric_docking::SymDockProtocol::set_view ( bool view_in)

References view_.

Referenced by SymDockProtocol().

void protocols::symmetric_docking::SymDockProtocol::task_factory ( core::pack::task::TaskFactoryOP task_factory)

References init_task_factory_.

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::task_factory ( ) const

References init_task_factory_.

core::pack::task::TaskFactoryOP & protocols::symmetric_docking::SymDockProtocol::task_factory ( )

References init_task_factory_.

Member Data Documentation

bool protocols::symmetric_docking::SymDockProtocol::autofoldtree_

private

should docking change the foldtree?

bool protocols::symmetric_docking::SymDockProtocol::design_

private

Referenced by apply(), and design().

bool protocols::symmetric_docking::SymDockProtocol::dock_ppk_

private

Referenced by set_default(), and set_dock_ppk().

protocols::symmetric_docking::SymDockingHiResOP protocols::symmetric_docking::SymDockProtocol::docking_high_

private

Referenced by apply(), and set_highres_scorefxn().

protocols::symmetric_docking::SymDockingLowResOP protocols::symmetric_docking::SymDockProtocol::docking_low_

private

Referenced by apply(), and set_lowres_scorefxn().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_

private

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_high_min_

private

Referenced by apply(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_low_

private

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), set_default(), set_lowres_scorefxn(), and SymDockProtocol().

core::scoring::ScoreFunctionOP protocols::symmetric_docking::SymDockProtocol::docking_score_pack_

private

Referenced by apply(), recover_sidechains(), set_default(), set_highres_scorefxn(), and SymDockProtocol().

bool protocols::symmetric_docking::SymDockProtocol::fullatom_

private

information about the mode

Referenced by apply(), calc_interaction_energy(), clone(), score_only(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::hurry_

private

Referenced by apply(), and hurry().

core::pack::task::TaskFactoryOP protocols::symmetric_docking::SymDockProtocol::init_task_factory_

private

Referenced by apply(), and task_factory().

bool protocols::symmetric_docking::SymDockProtocol::local_refine_

private

Referenced by apply(), clone(), and set_local_refine().

Size protocols::symmetric_docking::SymDockProtocol::max_repeats_

private

Referenced by set_max_repeats().

moves::MonteCarloOP protocols::symmetric_docking::SymDockProtocol::mc_

private

utility::vector1<core::Size> protocols::symmetric_docking::SymDockProtocol::movable_jumps_

private

the jump number across which to do rigid_body transformations

bool protocols::symmetric_docking::SymDockProtocol::passed_highres_filter_

private

Referenced by apply(), set_default(), and set_fullatom().

bool protocols::symmetric_docking::SymDockProtocol::passed_lowres_filter_

private

Referenced by apply(), set_default(), and set_local_refine().

bool protocols::symmetric_docking::SymDockProtocol::rtmin_

private

Referenced by recover_sidechains(), and set_dock_rtmin().

bool protocols::symmetric_docking::SymDockProtocol::sc_min_

private

Referenced by set_sc_min().

std::map< std::string, core::Real > protocols::symmetric_docking::SymDockProtocol::score_map_

private

Referenced by apply(), and docking_highres_filter().

bool protocols::symmetric_docking::SymDockProtocol::view_

private

whether or not to initialize the viewer (for opengl)

Referenced by clone(), and set_view().

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

src/protocols/symmetric_docking/SymDockProtocol.hh
src/protocols/symmetric_docking/SymDockProtocol.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation