this mover does the high resolution refinement stage of the RosettaDock algorithm More...

#include <DockingHighResLegacy.hh>

Public Member Functions
	DockingHighResLegacy ()

	DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionOP scorefxn)

	DockingHighResLegacy (int rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)

	DockingHighResLegacy (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)

	~DockingHighResLegacy ()

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

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

void	set_move_map (core::kinematics::MoveMapOP movemap_in)

void	set_min_type (std::string min_type_in)

void	set_repack (bool repack_switch)

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

virtual void	set_task_factory (core::pack::task::TaskFactoryOP task)

void	define_loops (core::pose::Pose const &pose, loops::LoopsOP loop_set, Real &interface_dist)

void	set_trans_magnitude (core::Real trans_magnitude)

void	set_rot_magnitude (core::Real rot_magnitude)

void	set_rt_min (bool rt_min)

bool	rt_min ()

void	set_sc_min (bool sc_min)

bool	sc_min ()

moves::MonteCarloOP	get_mc ()

core::Real	get_trans_magnitude ()

core::Real	get_rot_magnitude ()

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

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

void	set_dock_min_protocol ()
	main entrance for normal rigid-body minimization More...

void	set_dock_mcm_protocol (core::pose::Pose &pose)
	main entrance to do monte carlo minimization More...

void	set_dock_ppk_protocol (core::pose::Pose &pose)
	main entrance to prepacking for docking More...

void	design (bool const des)

bool	design () const

Public Member Functions inherited from protocols::docking::DockingHighRes
	DockingHighRes ()
	Default constructor. More...

	DockingHighRes (core::Size const rb_jump)
	Constructor with one argument - the jump number to dock over. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
	Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing. More...

	DockingHighRes (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with three arguments. The first is the DockJumps, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing. More...

	DockingHighRes (DockingHighRes const &old_instance)

virtual	~DockingHighRes ()

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

void	set_ignore_default_task (bool ignore_default_task)

bool	ignore_default_task ()

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

void	set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)

DockJumps &	movable_jumps ()

DockJumps const &	movable_jumps () const

core::pack::task::TaskFactoryCOP	task_factory ()

void	set_sc_min (bool sc_min)

void	set_rt_min (bool rt_min)

void	set_partners (std::string partners)

void	set_interface_definition_task_operation (protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)

void	set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

void	add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)

utility::vector1 < core::pack::task::operation::TaskOperationOP >	get_additional_task_operarations ()

bool	sc_min ()

bool	rt_min ()

std::string	partners ()

core::scoring::ScoreFunctionOP	scorefxn () const

core::scoring::ScoreFunctionOP	scorefxn_pack () 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 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

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

Private Types
typedef core::Real	Real

Private Member Functions
void	setup_packing (core::pose::Pose &pose)
	utility function to set up packer options for internal task factory More...

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::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP	tf2 ()

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 high resolution refinement stage of the RosettaDock algorithm

Member Typedef Documentation

typedef core::Real protocols::docking::DockingHighResLegacy::Real

private

Constructor & Destructor Documentation

protocols::docking::DockingHighResLegacy::DockingHighResLegacy ( )

References design_, init_task_factory_, and protocols::moves::Mover::type().

Referenced by clone().

protocols::docking::DockingHighResLegacy::DockingHighResLegacy	(	int	rb_jump,
		core::scoring::ScoreFunctionOP	scorefxn
	)

References design_, init_task_factory_, and protocols::moves::Mover::type().

protocols::docking::DockingHighResLegacy::DockingHighResLegacy	(	int	rb_jump,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::scoring::ScoreFunctionOP	scorefxn_pack
	)

References design_, init_task_factory_, and protocols::moves::Mover::type().

protocols::docking::DockingHighResLegacy::DockingHighResLegacy	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::scoring::ScoreFunctionOP	scorefxn_pack
	)

References design_, init_task_factory_, and protocols::moves::Mover::type().

protocols::docking::DockingHighResLegacy::~DockingHighResLegacy ( )

Member Function Documentation

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

virtual

docking high resolution apply function

Detailed:: decides what to call according to options

Implements protocols::docking::DockingHighRes.

References protocols::moves::SequenceMover::apply(), docking_highres_protocol_mover_, mc_, option, protocols::moves::MonteCarlo::recover_low(), protocols::moves::MonteCarlo::reset(), scoring, set_default(), and protocols::TR.

protocols::moves::MoverOP protocols::docking::DockingHighResLegacy::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 DockingHighResLegacy().

Referenced by set_dock_mcm_protocol().

void protocols::docking::DockingHighResLegacy::define_loops	(	core::pose::Pose const &	pose,
		loops::LoopsOP	loop_set,
		Real &	interface_dist
	)

References protocols::loops::Loops::add_loop(), protocols::loops::Loops::choose_cutpoints(), protocols::loops::Loops::clear(), protocols::docking::DockingHighRes::movable_jumps(), nres, core::pose::Pose::pdb_info(), core::pack::task::TaskFactory::push_back(), core::pose::Pose::total_residue(), and protocols::TR.

Referenced by set_dock_mcm_protocol().

void protocols::docking::DockingHighResLegacy::design ( bool const des )

References design_.

bool protocols::docking::DockingHighResLegacy::design ( ) const

References design_.

moves::MonteCarloOP protocols::docking::DockingHighResLegacy::get_mc ( )

References mc_.

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

virtual

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

Implements protocols::docking::DockingHighRes.

core::Real protocols::docking::DockingHighResLegacy::get_rot_magnitude ( )

inline

References rot_magnitude_.

core::Real protocols::docking::DockingHighResLegacy::get_trans_magnitude ( )

inline

References trans_magnitude_.

bool protocols::docking::DockingHighResLegacy::rt_min ( )

inline

References rt_min_.

Referenced by set_dock_mcm_protocol(), set_dock_ppk_protocol(), and set_rt_min().

bool protocols::docking::DockingHighResLegacy::sc_min ( )

inline

References sc_min_.

Referenced by set_dock_mcm_protocol(), set_dock_ppk_protocol(), and set_sc_min().

void protocols::docking::DockingHighResLegacy::set_default ( core::pose::Pose & pose )

void protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol ( core::pose::Pose & pose )

main entrance to do monte carlo minimization

dock_mcm_protocol

Detailed:: a total of 50 cycles of monte-carlo minimization will be carried out if the minimized structure can pass the filter after the first and fifth cycle. Then it is rigid-body minimized to a stringent tolerance.

Remarks

References: docking_mcm_protocol from docking_minimize.cc: pose_docking_monte_carlo_minimize from pose_docking.cc

Authors: Sid Chaudhury May 28 2009

Last Modified: April 30 2008

References protocols::moves::MoverContainer::add_mover(), clone(), define_loops(), docking_highres_protocol_mover_, exit, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::moves::Mover::get_input_pose(), init_task_factory_, initial_repack, mc_, min_tolerance_, min_type_, minimization_threshold, protocols::docking::DockingHighRes::movable_jumps(), movemap_, nb_list_, option, protocols::rigid::partner_downstream, repack_period_, repack_switch_, rot_magnitude_, rt_min(), rtmin, sc_min(), protocols::docking::DockingHighRes::scorefxn(), protocols::docking::DockingHighRes::scorefxn_pack(), set_task_factory(), protocols::docking::DockingHighRes::task_factory(), protocols::simple_moves::PackRotamersMover::task_factory(), core::pose::Pose::total_residue(), protocols::TR, and trans_magnitude_.

Referenced by set_protocol().

void protocols::docking::DockingHighResLegacy::set_dock_min_protocol ( )

main entrance for normal rigid-body minimization

minimize_trial

Detailed:: retrieve the structure in the low array and do the normal minimization by calling using a min_mover to optimize the score accourding to the scorefunction that has been set

Remarks

References: docking_minimize_trial from docking_minimize.cc: pose_docking_minimize_trial from pose_docking.cc

Authors: Monica Berrondo June 14 2007

Last Modified: October 15 2007

References protocols::moves::MoverContainer::add_mover(), docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, protocols::docking::DockingHighRes::scorefxn(), and protocols::TR.

Referenced by set_protocol().

void protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol ( core::pose::Pose & pose )

main entrance to prepacking for docking

dock_ppk_protocol

Detailed:: does a full repack of all sidechains for each partner after moving them away by 500A, then it brings them back together

Remarks

References: pose_docking_prepack_protocol from pose_docking.cc

Authors: Sid Chaudhury October 3 2008

Last Modified: October 3 2008

References protocols::moves::MoverContainer::add_mover(), begin, docking_highres_protocol_mover_, protocols::docking::DockingHighRes::movable_jumps(), rt_min(), sc_min(), protocols::docking::DockingHighRes::scorefxn_pack(), protocols::docking::DockingHighRes::task_factory(), protocols::TR, and trans_magnitude.

void protocols::docking::DockingHighResLegacy::set_min_type ( std::string min_type_in )

References min_type_.

void protocols::docking::DockingHighResLegacy::set_move_map ( core::kinematics::MoveMapOP movemap_in )

References movemap_.

void protocols::docking::DockingHighResLegacy::set_protocol ( core::pose::Pose & pose )

References utility::exit(), option, set_dock_mcm_protocol(), and set_dock_min_protocol().

Referenced by set_default().

void protocols::docking::DockingHighResLegacy::set_repack ( bool repack_switch )

References repack_switch_.

void protocols::docking::DockingHighResLegacy::set_rot_magnitude ( core::Real rot_magnitude )

References rot_magnitude_.

Referenced by set_default().

void protocols::docking::DockingHighResLegacy::set_rt_min ( bool rt_min )

inline

References rt_min(), and rt_min_.

void protocols::docking::DockingHighResLegacy::set_sc_min ( bool sc_min )

inline

References sc_min(), and sc_min_.

void protocols::docking::DockingHighResLegacy::set_task_factory ( core::pack::task::TaskFactoryOP task )

virtual

References init_task_factory_.

Referenced by set_dock_mcm_protocol(), and setup_packing().

void protocols::docking::DockingHighResLegacy::set_trans_magnitude ( core::Real trans_magnitude )

References trans_magnitude_.

Referenced by set_default().

void protocols::docking::DockingHighResLegacy::setup_packing ( core::pose::Pose & pose )

private

utility function to set up packer options for internal task factory

References chain, core::conformation::Residue::chain(), core::kinematics::FoldTree::cutpoint_by_jump(), design_, core::pose::Pose::fold_tree(), init_task_factory_, core::pack::dunbrack::load_unboundrot(), protocols::docking::DockingHighRes::movable_jumps(), core::pose::Pose::num_jump(), option, core::pose::Pose::residue(), set_task_factory(), protocols::TR, unboundrot, and user.

Referenced by set_default().

Member Data Documentation

bool protocols::docking::DockingHighResLegacy::bb_

private

Referenced by set_default().

bool protocols::docking::DockingHighResLegacy::chi_

private

Referenced by set_default().

bool protocols::docking::DockingHighResLegacy::design_

private

Referenced by design(), DockingHighResLegacy(), and setup_packing().

moves::SequenceMoverOP protocols::docking::DockingHighResLegacy::docking_highres_protocol_mover_

private

Referenced by apply(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_dock_ppk_protocol().

core::pack::task::TaskFactoryOP protocols::docking::DockingHighResLegacy::init_task_factory_

private

Referenced by DockingHighResLegacy(), set_dock_mcm_protocol(), set_task_factory(), and setup_packing().

moves::MonteCarloOP protocols::docking::DockingHighResLegacy::mc_

private

Referenced by apply(), get_mc(), set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().

core::Real protocols::docking::DockingHighResLegacy::min_tolerance_

private

Referenced by set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().

std::string protocols::docking::DockingHighResLegacy::min_type_

private

Referenced by set_default(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_min_type().

core::kinematics::MoveMapOP protocols::docking::DockingHighResLegacy::movemap_

private

Referenced by set_default(), set_dock_mcm_protocol(), set_dock_min_protocol(), and set_move_map().

bool protocols::docking::DockingHighResLegacy::nb_list_

private

Referenced by set_default(), set_dock_mcm_protocol(), and set_dock_min_protocol().

core::Size protocols::docking::DockingHighResLegacy::repack_period_

private

Referenced by set_default(), and set_dock_mcm_protocol().

bool protocols::docking::DockingHighResLegacy::repack_switch_

private

Referenced by set_default(), set_dock_mcm_protocol(), and set_repack().

core::Real protocols::docking::DockingHighResLegacy::rot_magnitude_

private

Referenced by get_rot_magnitude(), set_dock_mcm_protocol(), and set_rot_magnitude().

bool protocols::docking::DockingHighResLegacy::rt_min_

private

Referenced by rt_min(), and set_rt_min().

bool protocols::docking::DockingHighResLegacy::sc_min_

private

Referenced by sc_min(), and set_sc_min().

core::Real protocols::docking::DockingHighResLegacy::temperature_

private

Referenced by set_default().

core::Real protocols::docking::DockingHighResLegacy::trans_magnitude_

private

Referenced by get_trans_magnitude(), set_dock_mcm_protocol(), and set_trans_magnitude().

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

src/protocols/docking/DockingHighResLegacy.hh
src/protocols/docking/DockingHighResLegacy.cc

Private Attributes
core::kinematics::MoveMapOP	movemap_

moves::SequenceMoverOP	docking_highres_protocol_mover_

moves::MonteCarloOP	mc_

core::Real	trans_magnitude_

core::Real	rot_magnitude_

bool	chi_

bool	bb_

bool	repack_switch_

bool	design_

bool	rt_min_

bool	sc_min_

core::pack::task::TaskFactoryOP	init_task_factory_

core::Size	repack_period_

core::Real	temperature_

core::Real	min_tolerance_

bool	nb_list_

std::string	min_type_

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation