#include <FullatomRelaxMover.hh>

Inheritance diagram for protocols::surface_docking::FullatomRelaxMover:

[legend]

Public Member Functions
	FullatomRelaxMover ()

	FullatomRelaxMover (FullatomRelaxMover const &src)

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

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

	~FullatomRelaxMover () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

void	set_nmoves (const core::Size)

std::string	get_sol_secondary_struct ()

std::string	get_ads_secondary_struct ()

void	set_surface_contact_mover (protocols::docking::FaDockingSlideIntoContactOP surface_contact_mover)

void	set_surface_orient_mover (SurfaceOrientMoverOP surface_orient)

void	set_surface_parameters (protocols::surface_docking::SurfaceParametersOP surface_parameters)

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

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

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

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	copy_data (FullatomRelaxMover object_to_copy_to, FullatomRelaxMover object_to_copy_from)

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

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

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

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

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

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

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

void	setup_defaults ()

void	setup_movers (const core::pose::Pose &pose)

void	set_smallmovesize (core::Size scale)

void	set_ljrepulsion_weight (core::Real weight_scale)

void	set_ecounter (core::Size ecount)

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

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

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

Private Attributes
core::Real	kT_

core::Size	nmoves_

core::Size	encounter_

core::Size	encounter_cycle_

std::map< char, core::Real >	angle_max_

core::scoring::ScoreFunctionOP	score_high_res_

std::string	small_min_type_

std::string	shear_min_type_

core::kinematics::MoveMapOP	move_map_

moves::MonteCarloOP	monte_carlo_

simple_moves::SmallMoverOP	small_mover_

minimization_packing::MinMoverOP	small_min_mover_

moves::SequenceMoverOP	small_sequence_mover_

moves::TrialMoverOP	small_trial_min_mover_

simple_moves::ShearMoverOP	shear_mover_

minimization_packing::MinMoverOP	shear_min_mover_

moves::SequenceMoverOP	shear_sequence_mover_

moves::TrialMoverOP	shear_trial_min_mover_

std::string	sol_sec_struct_

std::string	ads_sec_struct_

std::string	sec_struct_

protocols::docking::FaDockingSlideIntoContactOP	surface_contact_mover_

protocols::surface_docking::SurfaceOrientMoverOP	surface_orient_

protocols::surface_docking::SurfaceParametersOP	surface_parameters_

docking::DockMCMProtocolOP	dock_mcm_

core::Size	outer_loop_cycles_

core::Size	inner_loop_cycles_

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 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...

Constructor & Destructor Documentation

◆ FullatomRelaxMover() [1/2]

protocols::surface_docking::FullatomRelaxMover::FullatomRelaxMover ( )

References setup_defaults().

◆ FullatomRelaxMover() [2/2]

protocols::surface_docking::FullatomRelaxMover::FullatomRelaxMover ( FullatomRelaxMover const & src )

References copy_data().

◆ ~FullatomRelaxMover()

protocols::surface_docking::FullatomRelaxMover::~FullatomRelaxMover ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::surface_docking::FullatomRelaxMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ads_sec_struct_, calc_secondary_struct(), refinement_cycle(), sec_struct_, set_ecounter(), set_ljrepulsion_weight(), set_smallmovesize(), and setup_movers().

◆ calc_secondary_struct()

void protocols::surface_docking::FullatomRelaxMover::calc_secondary_struct ( core::pose::Pose & pose )

private

References protocols::simple_filters::dssp(), core::pose::Pose::num_jump(), sec_struct_, core::pose::Pose::set_secstruct(), and core::pose::Pose::split_by_chain().

Referenced by apply(), output_solution_state(), and refinement_cycle().

◆ clone()

protocols::moves::MoverOP protocols::surface_docking::FullatomRelaxMover::clone ( ) const

overridevirtual

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.

◆ copy_data()

void protocols::surface_docking::FullatomRelaxMover::copy_data	(	FullatomRelaxMover	object_to_copy_to,
		FullatomRelaxMover	object_to_copy_from
	)

private

◆ dock_mcm_on_surface()

void protocols::surface_docking::FullatomRelaxMover::dock_mcm_on_surface ( core::pose::Pose & pose )

private

References dock_mcm_, and protocols::TR().

Referenced by refinement_cycle().

◆ fresh_instance()

protocols::moves::MoverOP protocols::surface_docking::FullatomRelaxMover::fresh_instance ( ) const

overridevirtual

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.

◆ get_ads_secondary_struct()

std::string protocols::surface_docking::FullatomRelaxMover::get_ads_secondary_struct ( )

References ads_sec_struct_.

◆ get_name()

std::string protocols::surface_docking::FullatomRelaxMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_sol_secondary_struct()

std::string protocols::surface_docking::FullatomRelaxMover::get_sol_secondary_struct ( )

References sol_sec_struct_.

◆ inner_loop_refinement()

void protocols::surface_docking::FullatomRelaxMover::inner_loop_refinement ( core::pose::Pose & pose )

private

References set_secondary_struct(), shear_min_mover_, shear_trial_min_mover_, small_min_mover_, and small_trial_min_mover_.

Referenced by outer_loop_refinement_solution().

◆ outer_loop_refinement_adsorbed()

void protocols::surface_docking::FullatomRelaxMover::outer_loop_refinement_adsorbed ( core::pose::Pose & pose )

private

References outer_loop_refinement_solution(), surface_contact_mover_, surface_orient_, and protocols::TR().

Referenced by refinement_cycle().

◆ outer_loop_refinement_solution()

void protocols::surface_docking::FullatomRelaxMover::outer_loop_refinement_solution ( core::pose::Pose & pose )

private

References inner_loop_cycles_, inner_loop_refinement(), set_secondary_struct(), shear_min_mover_, shear_trial_min_mover_, small_min_mover_, and small_trial_min_mover_.

Referenced by outer_loop_refinement_adsorbed(), and refinement_cycle().

◆ output_solution_state()

void protocols::surface_docking::FullatomRelaxMover::output_solution_state ( core::pose::Pose & pose )

private

References protocols::jd2::add_string_real_pair_to_current_job(), protocols::jd2::add_string_string_pair_to_current_job(), calc_secondary_struct(), core::pose::Pose::energies(), monte_carlo_, protocols::jd2::output_intermediate_pose(), sec_struct_, sol_sec_struct_, core::scoring::Energies::total_energy(), and protocols::TR().

Referenced by refinement_cycle().

◆ refinement_cycle()

void protocols::surface_docking::FullatomRelaxMover::refinement_cycle ( core::pose::Pose & pose )

private

References calc_secondary_struct(), dock_mcm_on_surface(), encounter_, encounter_cycle_, monte_carlo_, move_map_, core::pose::Pose::num_jump(), outer_loop_cycles_, outer_loop_refinement_adsorbed(), outer_loop_refinement_solution(), output_solution_state(), reorient_and_slide_into_surface(), and protocols::TR().

Referenced by apply().

◆ reorient_and_slide_into_surface()

void protocols::surface_docking::FullatomRelaxMover::reorient_and_slide_into_surface ( core::pose::Pose & pose )

private

References protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), monte_carlo_, core::pose::Pose::num_jump(), protocols::rigid::partner_upstream, reposition_above_surface(), surface_contact_mover_, surface_orient_, and protocols::TR().

Referenced by refinement_cycle().

◆ reposition_above_surface()

void protocols::surface_docking::FullatomRelaxMover::reposition_above_surface ( core::pose::Pose & pose )

private

References protocols::rigid::RigidBodyTransMover::apply(), protocols::geometry::centroids_by_jump(), core::pose::Pose::num_jump(), protocols::rigid::RigidBodyTransMover::step_size(), and surface_parameters_.

Referenced by reorient_and_slide_into_surface().

◆ set_ecounter()

void protocols::surface_docking::FullatomRelaxMover::set_ecounter ( core::Size ecount )

private

References encounter_.

Referenced by apply().

◆ set_ljrepulsion_weight()

void protocols::surface_docking::FullatomRelaxMover::set_ljrepulsion_weight ( core::Real weight_scale )

private

References core::scoring::fa_rep, and score_high_res_.

Referenced by apply().

◆ set_nmoves()

void protocols::surface_docking::FullatomRelaxMover::set_nmoves ( const core::Size nmoves_in )

References nmoves_.

◆ set_secondary_struct()

void protocols::surface_docking::FullatomRelaxMover::set_secondary_struct ( core::pose::Pose & pose )

private

References core::pose::Pose::num_jump(), sec_struct_, and core::pose::Pose::set_secstruct().

Referenced by inner_loop_refinement(), and outer_loop_refinement_solution().

◆ set_smallmovesize()

void protocols::surface_docking::FullatomRelaxMover::set_smallmovesize ( core::Size scale )

private

References small_mover_.

Referenced by apply().

◆ set_surface_contact_mover()

void protocols::surface_docking::FullatomRelaxMover::set_surface_contact_mover ( protocols::docking::FaDockingSlideIntoContactOP surface_contact_mover )

References surface_contact_mover_.