#include <DockingLowRes.hh>

Inheritance diagram for protocols::docking::DockingLowRes:

Collaboration diagram for protocols::docking::DockingLowRes:

Public Member Functions
	DockingLowRes ()
	Default constructor. More...

	~DockingLowRes ()

	DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1)
	Constructor with two arguments. The first is scorefunction to be used for docking, the second is the jump to dock over. More...

	DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps)
	Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More...

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

void	set_default ()
	Assigns default values to primitive members. More...

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

void	sync_objects_with_flags ()
	Instantiates non-primitive members based on the value of the primitive members. More...

moves::MonteCarloOP	get_mc ()

virtual void	apply (core::pose::Pose &pose)
	Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...

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

void	rigid_body_trial (core::pose::Pose &pose)
	Perform a cycle of rigid-body Monte Carlo moves. More...

void	set_inner_cycles (core::Size inner_cycles)

void	set_outer_cycles (core::Size outer_cycles)

virtual void	show (std::ostream &out=std::cout) 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

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

Public Attributes
bool	flags_and_objects_are_in_sync_

bool	first_apply_with_current_setup_

DockJumps	movable_jumps_

protocols::moves::SequenceMoverOP	docking_lowres_protocol_

core::scoring::ScoreFunctionCOP	scorefxn_

Protected Member Functions
virtual void	finalize_setup (core::pose::Pose &pose)
	Performs the portion of setup of non-primitive members that requires a pose - called on apply. 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...

Private Member Functions
void	init (DockJumps const movable_jumps, core::scoring::ScoreFunctionCOP scorefxn)
	Sets up the instance of DockingLowRes and initializes all members based on values passed in at construction or via the command line. More...

Friends
std::ostream &	operator<< (std::ostream &out, const DockingLowRes &dp)

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...

Detailed Description

Definition at line 53 of file DockingLowRes.hh.

Constructor & Destructor Documentation

protocols::docking::DockingLowRes::DockingLowRes ( )

Default constructor.

Definition at line 78 of file DockingLowRes.cc.

References init().

Referenced by clone().

protocols::docking::DockingLowRes::~DockingLowRes ( )

Definition at line 124 of file DockingLowRes.cc.

protocols::docking::DockingLowRes::DockingLowRes	(	core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size const	rb_jump = `1`
	)

Constructor with two arguments. The first is scorefunction to be used for docking, the second is the jump to dock over.

Definition at line 86 of file DockingLowRes.cc.

References init().

protocols::docking::DockingLowRes::DockingLowRes	(	core::scoring::ScoreFunctionCOP	scorefxn,
		DockJumps const	movable_jumps
	)

Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps.

Definition at line 94 of file DockingLowRes.cc.

References init().

Member Function Documentation

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

virtual

Perform several cycles of rigid-body Monte Carlo moves and adapt the step size.

DockingLowRes.apply

Detailed:

Remarks: currently used only in the low-resolution step (centroid mode)

References: pose_docking_centroid_rigid_body_adaptive from pose_docking.cc and: rigid_body_MC_cycle_adaptive from dock_structure.cc

Authors: Monica Berrondo October 22 2007

Last Modified: October 22 2007

Implements protocols::moves::Mover.

Definition at line 199 of file DockingLowRes.cc.

References accept_rate_, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, mc_, outer_cycles_, rigid_body_trial(), rot_magnitude_, show(), sync_objects_with_flags(), protocols::TR(), and trans_magnitude_.

protocols::moves::MoverOP protocols::docking::DockingLowRes::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.

Reimplemented in protocols::docking::DockingLowResEnsemble.

Definition at line 127 of file DockingLowRes.cc.

References DockingLowRes().

void protocols::docking::DockingLowRes::finalize_setup ( core::pose::Pose & pose)

protectedvirtual

Performs the portion of setup of non-primitive members that requires a pose - called on apply.

Reimplemented in protocols::docking::DockingLowResEnsemble.

Definition at line 173 of file DockingLowRes.cc.

References docking_lowres_protocol_, movemap_, protocols::rigid::n2c, rb_mover_, rot_magnitude_, and trans_magnitude_.

Referenced by apply(), and protocols::docking::DockingLowResEnsemble::finalize_setup().

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

Definition at line 291 of file DockingLowRes.cc.

References mc_.

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 241 of file DockingLowRes.cc.

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

void protocols::docking::DockingLowRes::init	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

private

Sets up the instance of DockingLowRes and initializes all members based on values passed in at construction or via the command line.

Definition at line 102 of file DockingLowRes.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), movable_jumps_, scorefxn_, set_default(), sync_objects_with_flags(), and protocols::moves::Mover::type().

Referenced by DockingLowRes().

void protocols::docking::DockingLowRes::rigid_body_trial ( core::pose::Pose & pose)

Perform a cycle of rigid-body Monte Carlo moves.

rigid_body_trial

Detailed: Performs a number (nattempts) of MC rigid-body moves: (of size trans_magnitude, rot_magnitude). The number of successful attempts is stored in accept_rate_ and used in adaptive trials.

Remarks: the success_rate defines whether the translation/rotation size is increased or decreased for the next cycle. currently used only in the low-resolution step (centroid mode)

References: pose_docking_rigid_body_trial from pose_docking.cc and: rigid_body_MC_cycle from dock_structure.cc

Authors: Monica Berrondo October 22 2007

Last Modified: October 22 2007

Definition at line 266 of file DockingLowRes.cc.

References accept_rate_, protocols::moves::accept_reject, docking_lowres_protocol_, inner_cycles_, mc_, rb_mover_, rot_magnitude_, and trans_magnitude_.

Referenced by apply().

void protocols::docking::DockingLowRes::set_default ( )

Assigns default values to primitive members.

Definition at line 132 of file DockingLowRes.cc.

References accept_rate_, bb_, chi_, inner_cycles_, nb_list_, outer_cycles_, rot_magnitude_, temperature_, and trans_magnitude_.

Referenced by init().

void protocols::docking::DockingLowRes::set_inner_cycles ( core::Size inner_cycles)

inline

Definition at line 97 of file DockingLowRes.hh.

References inner_cycles_.

void protocols::docking::DockingLowRes::set_outer_cycles ( core::Size outer_cycles)

inline

Definition at line 98 of file DockingLowRes.hh.

References outer_cycles_.

void protocols::docking::DockingLowRes::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn)

Definition at line 166 of file DockingLowRes.cc.

References flags_and_objects_are_in_sync_, and scorefxn_.

void protocols::docking::DockingLowRes::show ( std::ostream & out = std::cout) const

virtual

Show the complete setup of the docking protocol

Reimplemented in protocols::docking::DockingLowResEnsemble.

Definition at line 296 of file DockingLowRes.cc.

References protocols::comparative_modeling::features::A, inner_cycles_, outer_cycles_, and scorefxn_.

Referenced by apply(), protocols::docking::operator<<(), and protocols::docking::DockingLowResEnsemble::show().

void protocols::docking::DockingLowRes::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

Definition at line 146 of file DockingLowRes.cc.

References bb_, chi_, docking_lowres_protocol_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, mc_, movable_jumps_, movemap_, rb_mover_, scorefxn_, and temperature_.

Referenced by apply(), and init().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const DockingLowRes &	dp
	)

friend

Definition at line 322 of file DockingLowRes.cc.

Member Data Documentation

core::Real protocols::docking::DockingLowRes::accept_rate_

private

Definition at line 130 of file DockingLowRes.hh.

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

bool protocols::docking::DockingLowRes::bb_

private

Definition at line 132 of file DockingLowRes.hh.

Referenced by set_default(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::chi_

private

Definition at line 132 of file DockingLowRes.hh.

Referenced by set_default(), and sync_objects_with_flags().

protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::docking_lowres_protocol_

Definition at line 113 of file DockingLowRes.hh.

Referenced by protocols::docking::DockingLowResEnsemble::finalize_setup(), finalize_setup(), rigid_body_trial(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::first_apply_with_current_setup_

Definition at line 106 of file DockingLowRes.hh.

Referenced by apply(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::flags_and_objects_are_in_sync_

Definition at line 105 of file DockingLowRes.hh.

Referenced by apply(), set_scorefxn(), and sync_objects_with_flags().

core::Size protocols::docking::DockingLowRes::inner_cycles_

private

Definition at line 131 of file DockingLowRes.hh.

Referenced by rigid_body_trial(), set_default(), set_inner_cycles(), and show().

protocols::moves::MonteCarloOP protocols::docking::DockingLowRes::mc_

private

Definition at line 125 of file DockingLowRes.hh.

Referenced by apply(), get_mc(), rigid_body_trial(), and sync_objects_with_flags().

DockJumps protocols::docking::DockingLowRes::movable_jumps_

Definition at line 110 of file DockingLowRes.hh.

Referenced by init(), and sync_objects_with_flags().

core::kinematics::MoveMapOP protocols::docking::DockingLowRes::movemap_

private

Definition at line 123 of file DockingLowRes.hh.

Referenced by finalize_setup(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::nb_list_

private

Definition at line 132 of file DockingLowRes.hh.

Referenced by set_default().

core::Size protocols::docking::DockingLowRes::outer_cycles_

private

Definition at line 131 of file DockingLowRes.hh.

Referenced by apply(), set_default(), set_outer_cycles(), and show().

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::rb_mover_

private

Definition at line 124 of file DockingLowRes.hh.

Referenced by finalize_setup(), rigid_body_trial(), and sync_objects_with_flags().

core::Real protocols::docking::DockingLowRes::rot_magnitude_

private

Definition at line 130 of file DockingLowRes.hh.

Referenced by apply(), finalize_setup(), rigid_body_trial(), and set_default().

core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::scorefxn_

Definition at line 114 of file DockingLowRes.hh.

Referenced by init(), set_scorefxn(), show(), and sync_objects_with_flags().

core::Real protocols::docking::DockingLowRes::temperature_

private

Definition at line 133 of file DockingLowRes.hh.

Referenced by set_default(), and sync_objects_with_flags().

core::Real protocols::docking::DockingLowRes::trans_magnitude_

private

Definition at line 130 of file DockingLowRes.hh.

Referenced by apply(), finalize_setup(), rigid_body_trial(), and set_default().

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

src/protocols/docking/DockingLowRes.hh
src/protocols/docking/DockingLowRes.cc

Private Attributes
core::kinematics::MoveMapOP	movemap_

protocols::rigid::RigidBodyPerturbNoCenterMoverOP	rb_mover_

protocols::moves::MonteCarloOP	mc_

core::Real	trans_magnitude_

core::Real	rot_magnitude_

core::Real	accept_rate_

core::Size	inner_cycles_

core::Size	outer_cycles_

bool	chi_

bool	bb_

bool	nb_list_

core::Real	temperature_

Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation