An optimized mover for Monte Carlo trial of rigid body perturbations. More...

#include <RigidSearchMover.hh>

Inheritance diagram for protocols::ligand_docking::RigidSearchMover:

Collaboration diagram for protocols::ligand_docking::RigidSearchMover:

Public Member Functions
	RigidSearchMover (int jump_id, int num_trials, core::scoring::ScoreFunctionCOP scorefxn)

	RigidSearchMover (RigidSearchMover const &that)

virtual	~RigidSearchMover ()

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

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

bool	recover_low () const
	Will the absolute lowest-energy pose be recovered at the end of apply()? More...

void	recover_low (bool b)
	Should the absolute lowest-energy pose be recovered at the end of apply()? More...

core::Real	translation () const
	Amount of random (Gaussian) translation, in Angstroms. More...

void	translation (core::Real angstroms)
	Amount of random (Gaussian) translation, in Angstroms. More...

core::Real	rotation () const
	Amount of random (Gaussian) rotation, in degrees. More...

void	rotation (core::Real degrees)
	Amount of random (Gaussian) rotation, in degrees. More...

void	rotate_around_downstream_centroid ()
	Rotation occurs around centroid of downstream half of the jump (default) More...

void	rotate_around_atom (core::Size rsd, core::Size atom)
	Rotation occurs around the specified atom. 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 MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

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 Attributes
int	jump_id_

int	num_trials_

core::scoring::ScoreFunctionCOP	scorefxn_

core::Real	temperature_

core::Real	rotate_deg_

core::Real	translate_Ang_

core::Size	rotate_rsd_

core::Size	rotate_atom_

bool	recover_low_

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

An optimized mover for Monte Carlo trial of rigid body perturbations.

Definition at line 36 of file RigidSearchMover.hh.

Constructor & Destructor Documentation

protocols::ligand_docking::RigidSearchMover::RigidSearchMover	(	int	jump_id,
		int	num_trials,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

Definition at line 44 of file RigidSearchMover.cc.

protocols::ligand_docking::RigidSearchMover::RigidSearchMover ( RigidSearchMover const & that)

Definition at line 60 of file RigidSearchMover.cc.

protocols::ligand_docking::RigidSearchMover::~RigidSearchMover ( )

virtual

Definition at line 76 of file RigidSearchMover.cc.

Member Function Documentation

void protocols::ligand_docking::RigidSearchMover::apply ( core::pose::Pose & pose)

virtual

std::string protocols::ligand_docking::RigidSearchMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 139 of file RigidSearchMover.cc.

bool protocols::ligand_docking::RigidSearchMover::recover_low ( ) const

inline

Will the absolute lowest-energy pose be recovered at the end of apply()?

Definition at line 48 of file RigidSearchMover.hh.

References recover_low_.

void protocols::ligand_docking::RigidSearchMover::recover_low ( bool b)

inline

Should the absolute lowest-energy pose be recovered at the end of apply()?

Definition at line 50 of file RigidSearchMover.hh.

References protocols::match::upstream::b, and recover_low_.

void protocols::ligand_docking::RigidSearchMover::rotate_around_atom	(	core::Size	rsd,
		core::Size	atom
	)

inline

Rotation occurs around the specified atom.

Definition at line 65 of file RigidSearchMover.hh.

References rotate_atom_, and rotate_rsd_.

void protocols::ligand_docking::RigidSearchMover::rotate_around_downstream_centroid ( )

inline

Rotation occurs around centroid of downstream half of the jump (default)

Definition at line 63 of file RigidSearchMover.hh.

References rotate_atom_, and rotate_rsd_.

core::Real protocols::ligand_docking::RigidSearchMover::rotation ( ) const

inline

Amount of random (Gaussian) rotation, in degrees.

Definition at line 58 of file RigidSearchMover.hh.

References rotate_deg_.

void protocols::ligand_docking::RigidSearchMover::rotation ( core::Real degrees)

inline

Amount of random (Gaussian) rotation, in degrees.

Definition at line 60 of file RigidSearchMover.hh.

References rotate_deg_.

core::Real protocols::ligand_docking::RigidSearchMover::translation ( ) const

inline

Amount of random (Gaussian) translation, in Angstroms.

Definition at line 53 of file RigidSearchMover.hh.

References translate_Ang_.

void protocols::ligand_docking::RigidSearchMover::translation ( core::Real angstroms)

inline

Amount of random (Gaussian) translation, in Angstroms.

Definition at line 55 of file RigidSearchMover.hh.

References translate_Ang_.

Member Data Documentation

int protocols::ligand_docking::RigidSearchMover::jump_id_

private

Definition at line 68 of file RigidSearchMover.hh.

Referenced by apply().

int protocols::ligand_docking::RigidSearchMover::num_trials_

private

Definition at line 69 of file RigidSearchMover.hh.

Referenced by apply().

bool protocols::ligand_docking::RigidSearchMover::recover_low_

private

Definition at line 77 of file RigidSearchMover.hh.

Referenced by apply(), and recover_low().

core::Size protocols::ligand_docking::RigidSearchMover::rotate_atom_

private

Definition at line 76 of file RigidSearchMover.hh.

Referenced by apply(), rotate_around_atom(), and rotate_around_downstream_centroid().

core::Real protocols::ligand_docking::RigidSearchMover::rotate_deg_

private

Definition at line 72 of file RigidSearchMover.hh.

Referenced by apply(), and rotation().

core::Size protocols::ligand_docking::RigidSearchMover::rotate_rsd_

private

Definition at line 75 of file RigidSearchMover.hh.

Referenced by apply(), rotate_around_atom(), and rotate_around_downstream_centroid().

core::scoring::ScoreFunctionCOP protocols::ligand_docking::RigidSearchMover::scorefxn_

private

Definition at line 70 of file RigidSearchMover.hh.

Referenced by apply().

core::Real protocols::ligand_docking::RigidSearchMover::temperature_

private

Definition at line 71 of file RigidSearchMover.hh.

Referenced by apply().

core::Real protocols::ligand_docking::RigidSearchMover::translate_Ang_

private

Definition at line 73 of file RigidSearchMover.hh.

Referenced by apply(), and translation().

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

src/protocols/ligand_docking/RigidSearchMover.hh
src/protocols/ligand_docking/RigidSearchMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation