#include <SymDockingHiRes.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockingHiRes:

Collaboration diagram for protocols::symmetric_docking::SymDockingHiRes:

Public Member Functions
	SymDockingHiRes ()

	SymDockingHiRes (core::scoring::ScoreFunctionOP scorefxn_in, core::scoring::ScoreFunctionOP scorefxn_pack_in)

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

virtual	~SymDockingHiRes ()

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)

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)
	define the prepacking protocol More...

moves::MonteCarloOP	get_mc ()

void	design (bool const des)

bool	design () const

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

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

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 Types
typedef core::Real	Real

typedef core::conformation::symmetry::SymmetricConformation	SymmetricConformation

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

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

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionCOP	scorefxn_pack_

core::kinematics::MoveMapOP	movemap_

simple_moves::symmetry::SymMinMoverOP	min_mover_

moves::SequenceMoverOP	docking_highres_protocol_mover_

moves::MonteCarloOP	mc_

simple_moves::symmetry::SymPackRotamersMoverOP	pack_interface_repack_

simple_moves::symmetry::SymRotamerTrialsMoverOP	pack_rottrial_

core::Real	trans_magnitude_

core::Real	rot_magnitude_

bool	chi_

bool	bb_

bool	repack_switch_

bool	design_

bool	rtmin_

bool	scmin_

core::pack::task::TaskFactoryOP	tf_
	tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below More...

core::pack::task::TaskFactoryOP	init_task_factory_
	task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory More...

core::Size	repack_period_

core::Real	temperature_

core::Real	min_tolerance_

bool	nb_list_

std::string	min_type_

Additional Inherited Members
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

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...

Detailed Description

Definition at line 50 of file SymDockingHiRes.hh.

Member Typedef Documentation

typedef core::Real protocols::symmetric_docking::SymDockingHiRes::Real

private

Definition at line 52 of file SymDockingHiRes.hh.

typedef core::conformation::symmetry::SymmetricConformation protocols::symmetric_docking::SymDockingHiRes::SymmetricConformation

private

Definition at line 53 of file SymDockingHiRes.hh.

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

private

Definition at line 54 of file SymDockingHiRes.hh.

Constructor & Destructor Documentation

protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes ( )

Definition at line 113 of file SymDockingHiRes.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), design_, init_task_factory_, scorefxn_, scorefxn_pack_, and protocols::moves::Mover::type().

Referenced by clone().

protocols::symmetric_docking::SymDockingHiRes::SymDockingHiRes	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		core::scoring::ScoreFunctionOP	scorefxn_pack_in
	)

Definition at line 123 of file SymDockingHiRes.cc.

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

protocols::symmetric_docking::SymDockingHiRes::~SymDockingHiRes ( )

virtual

Definition at line 134 of file SymDockingHiRes.cc.

Member Function Documentation

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

virtual

docking high resolution apply function

Detailed:: decides what to call according to options

Implements protocols::moves::Mover.

Definition at line 329 of file SymDockingHiRes.cc.

References docking_highres_protocol_mover_, mc_, set_default(), and protocols::symmetric_docking::TR().

protocols::moves::MoverOP protocols::symmetric_docking::SymDockingHiRes::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.

Definition at line 137 of file SymDockingHiRes.cc.

References SymDockingHiRes().

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

Definition at line 162 of file SymDockingHiRes.cc.

References design_.

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

Definition at line 167 of file SymDockingHiRes.cc.

References design_.

moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::get_mc ( )

Definition at line 147 of file SymDockingHiRes.cc.

References mc_.

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 348 of file SymDockingHiRes.cc.

void protocols::symmetric_docking::SymDockingHiRes::set_default ( core::pose::Pose & pose)

Definition at line 170 of file SymDockingHiRes.cc.

References bb_, chi_, core::pose::symmetry::make_symmetric_movemap(), mc_, min_tolerance_, min_type_, movemap_, nb_list_, repack_period_, repack_switch_, rot_magnitude_, rtmin_, scmin_, scorefxn_, set_protocol(), setup_packing(), temperature_, and trans_magnitude_.

Referenced by apply().

void protocols::symmetric_docking::SymDockingHiRes::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, modified for symmetric docking by Ingemar Andre

Last Modified: April 30 2008

Definition at line 402 of file SymDockingHiRes.cc.

References core::pose::Pose::conformation(), docking_highres_protocol_mover_, core::pose::symmetry::is_symmetric(), mc_, min_tolerance_, min_type_, movemap_, nb_list_, repack_period_, repack_switch_, rot_magnitude_, scmin_, scorefxn_, scorefxn_pack_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), tf_, protocols::symmetric_docking::TR(), and trans_magnitude_.

Referenced by set_protocol().

void protocols::symmetric_docking::SymDockingHiRes::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, modified for symmetric docking by Ingemar Andre

Last Modified: October 15 2007

Definition at line 371 of file SymDockingHiRes.cc.

References docking_highres_protocol_mover_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, scorefxn_, and protocols::symmetric_docking::TR().

Referenced by set_protocol().

void protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol ( core::pose::Pose & pose)

define the prepacking protocol

Definition at line 598 of file SymDockingHiRes.cc.

References core::pose::Pose::conformation(), docking_highres_protocol_mover_, core::pose::symmetry::is_symmetric(), scmin_, scorefxn_pack_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), tf_, and protocols::symmetric_docking::TR().

Referenced by set_protocol().

void protocols::symmetric_docking::SymDockingHiRes::set_min_type ( std::string min_type_in)

Definition at line 141 of file SymDockingHiRes.cc.

References min_type_.

void protocols::symmetric_docking::SymDockingHiRes::set_move_map ( core::kinematics::MoveMapOP movemap_in)

Definition at line 214 of file SymDockingHiRes.cc.

References movemap_.

void protocols::symmetric_docking::SymDockingHiRes::set_protocol ( core::pose::Pose & pose)

Definition at line 217 of file SymDockingHiRes.cc.

References set_dock_mcm_protocol(), set_dock_min_protocol(), and set_dock_ppk_protocol().

Referenced by set_default().

void protocols::symmetric_docking::SymDockingHiRes::set_repack ( bool repack_switch)

Definition at line 144 of file SymDockingHiRes.cc.

References repack_switch_.

void protocols::symmetric_docking::SymDockingHiRes::setup_packing ( core::pose::Pose & pose)

private

utility function to set up packer options for internal task factory

Definition at line 563 of file SymDockingHiRes.cc.

References design_, init_task_factory_, core::pack::dunbrack::load_unboundrot(), tf_, and protocols::symmetric_docking::TR().

Referenced by set_default().

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

Definition at line 151 of file SymDockingHiRes.cc.

References init_task_factory_.

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

Definition at line 157 of file SymDockingHiRes.cc.

References init_task_factory_.

Member Data Documentation

bool protocols::symmetric_docking::SymDockingHiRes::bb_

private

Definition at line 127 of file SymDockingHiRes.hh.

Referenced by set_default().

bool protocols::symmetric_docking::SymDockingHiRes::chi_

private

Definition at line 127 of file SymDockingHiRes.hh.

Referenced by set_default().

bool protocols::symmetric_docking::SymDockingHiRes::design_

private

Definition at line 129 of file SymDockingHiRes.hh.

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

moves::SequenceMoverOP protocols::symmetric_docking::SymDockingHiRes::docking_highres_protocol_mover_

private

Definition at line 120 of file SymDockingHiRes.hh.

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

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

private

task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory

Definition at line 139 of file SymDockingHiRes.hh.

Referenced by setup_packing(), SymDockingHiRes(), and task_factory().

moves::MonteCarloOP protocols::symmetric_docking::SymDockingHiRes::mc_

private

Definition at line 121 of file SymDockingHiRes.hh.

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