protocols::surface_docking::FullatomRelaxMover Class Reference

#include <FullatomRelaxMover.hh>

Inheritance diagram for protocols::surface_docking::FullatomRelaxMover:

Collaboration diagram for protocols::surface_docking::FullatomRelaxMover:

Public Types
typedef core::Real	Real
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

Public Member Functions
	FullatomRelaxMover ()
	~FullatomRelaxMover ()
void	apply (core::pose::Pose &)
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	set_nmoves (const core::Size)
void	setup_defaults ()
void	setupMovers ()
void	FinalizeMovers (core::pose::Pose &)
void	init_from_options ()
void	set_smallmovesize (Size scale)
void	set_ljrepulsion_weight (core::Real weight_scale)
void	set_ecounter (core::Size ecount)
void	CalcSecondayStruct (core::pose::Pose &pose)
std::string	getSecondayStruct ()
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
bool	benchmark_
core::Real	temperature_
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	smallmin_type_
std::string	shearmin_type_
core::kinematics::MoveMapOP	moveMapOP_
core::kinematics::MoveMapOP	smallmoveMapOP_
core::kinematics::MoveMapOP	shearmoveMapOP_
moves::MonteCarloOP	monteCarlo_
moves::MonteCarloOP	smallmonteCarlo_
moves::MonteCarloOP	shearmonteCarlo_
simple_moves::SmallMoverOP	smallmover_
simple_moves::MinMoverOP	smallminmover_
moves::SequenceMoverOP	smallsequenceMover_
moves::TrialMoverOP	small_trial_min_mover_
simple_moves::ShearMoverOP	shearmover_
simple_moves::MinMoverOP	shearminmover_
moves::SequenceMoverOP	shearsequenceMover_
moves::TrialMoverOP	shear_trial_min_mover_
std::string	SecStruct_

Additional Inherited Members
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...

Member Typedef Documentation

typedef core::Real protocols::surface_docking::FullatomRelaxMover::Real

Constructor & Destructor Documentation

protocols::surface_docking::FullatomRelaxMover::FullatomRelaxMover

(

)

References kT_, nmoves_, setup_defaults(), temperature_, protocols::TR(), and protocols::moves::Mover::type().

protocols::surface_docking::FullatomRelaxMover::~FullatomRelaxMover

(

)

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

References protocols::surface_docking::FaSlideIntoSurface::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), CalcSecondayStruct(), protocols::jd2::JobDistributor::current_job(), docking, encounter_, encounter_cycle_, FinalizeMovers(), protocols::jd2::JobDistributor::get_instance(), protocols::jd2::JobDistributor::job_outputter(), monteCarlo_, moveMapOP_, core::pose::Pose::num_jump(), protocols::rigid::partner_upstream, SecStruct_, shear_trial_min_mover_, shearminmover_, small_trial_min_mover_, smallminmover_, and protocols::TR().

void protocols::surface_docking::FullatomRelaxMover::CalcSecondayStruct

(

core::pose::Pose &

pose)

References core::scoring::dssp::Dssp::insert_ss_into_pose(), and SecStruct_.

Referenced by apply().

void protocols::surface_docking::FullatomRelaxMover::FinalizeMovers

(

core::pose::Pose &

pose)

References core::chemical::ResidueType::is_protein(), kT_, monteCarlo_, moveMapOP_, core::pose::Pose::num_jump(), core::pose::Pose::residue_type(), score_high_res_, shear_trial_min_mover_, shearmonteCarlo_, shearsequenceMover_, small_trial_min_mover_, smallmonteCarlo_, smallsequenceMover_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

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

virtual

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

Implements protocols::moves::Mover.

std::string protocols::surface_docking::FullatomRelaxMover::getSecondayStruct

(

)

References SecStruct_.

void protocols::surface_docking::FullatomRelaxMover::init_from_options

(

)

References benchmark_.

void protocols::surface_docking::FullatomRelaxMover::set_ecounter

(

core::Size

ecount)

References encounter_.

void protocols::surface_docking::FullatomRelaxMover::set_ljrepulsion_weight

(

core::Real

weight_scale)

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

void protocols::surface_docking::FullatomRelaxMover::set_nmoves

(

const core::Size

nmoves_in)

References nmoves_.

void protocols::surface_docking::FullatomRelaxMover::set_smallmovesize

(

Size

scale)

References smallmover_.

void protocols::surface_docking::FullatomRelaxMover::setup_defaults

(

)

References benchmark_, core::scoring::ScoreFunctionFactory::create_score_function(), encounter_cycle_, core::scoring::hack_elec, protocols::RG(), score_high_res_, setupMovers(), shearmin_type_, smallmin_type_, and protocols::TR().

Referenced by FullatomRelaxMover().

void protocols::surface_docking::FullatomRelaxMover::setupMovers

(

)

References moveMapOP_, nmoves_, score_high_res_, shearmin_type_, shearminmover_, shearmover_, shearsequenceMover_, smallmin_type_, smallminmover_, smallmover_, smallsequenceMover_, and temperature_.

Referenced by setup_defaults().

Member Data Documentation

std::map< char, core::Real > protocols::surface_docking::FullatomRelaxMover::angle_max_

private

bool protocols::surface_docking::FullatomRelaxMover::benchmark_

private

Referenced by init_from_options(), and setup_defaults().

core::Size protocols::surface_docking::FullatomRelaxMover::encounter_

private

Referenced by apply(), and set_ecounter().

core::Size protocols::surface_docking::FullatomRelaxMover::encounter_cycle_

private

Referenced by apply(), and setup_defaults().

core::Real protocols::surface_docking::FullatomRelaxMover::kT_

private

Referenced by FinalizeMovers(), and FullatomRelaxMover().

moves::MonteCarloOP protocols::surface_docking::FullatomRelaxMover::monteCarlo_

private

Referenced by apply(), and FinalizeMovers().

core::kinematics::MoveMapOP protocols::surface_docking::FullatomRelaxMover::moveMapOP_

private

Referenced by apply(), FinalizeMovers(), and setupMovers().

core::Size protocols::surface_docking::FullatomRelaxMover::nmoves_

private

Referenced by FullatomRelaxMover(), set_nmoves(), and setupMovers().

core::scoring::ScoreFunctionOP protocols::surface_docking::FullatomRelaxMover::score_high_res_

private

Referenced by FinalizeMovers(), set_ljrepulsion_weight(), setup_defaults(), and setupMovers().

std::string protocols::surface_docking::FullatomRelaxMover::SecStruct_

private

Referenced by apply(), CalcSecondayStruct(), and getSecondayStruct().

moves::TrialMoverOP protocols::surface_docking::FullatomRelaxMover::shear_trial_min_mover_

private

Referenced by apply(), and FinalizeMovers().

std::string protocols::surface_docking::FullatomRelaxMover::shearmin_type_

private

Referenced by setup_defaults(), and setupMovers().

simple_moves::MinMoverOP protocols::surface_docking::FullatomRelaxMover::shearminmover_

private

Referenced by apply(), and setupMovers().

moves::MonteCarloOP protocols::surface_docking::FullatomRelaxMover::shearmonteCarlo_

private

Referenced by FinalizeMovers().

core::kinematics::MoveMapOP protocols::surface_docking::FullatomRelaxMover::shearmoveMapOP_

private

simple_moves::ShearMoverOP protocols::surface_docking::FullatomRelaxMover::shearmover_

private

Referenced by setupMovers().

moves::SequenceMoverOP protocols::surface_docking::FullatomRelaxMover::shearsequenceMover_

private

Referenced by FinalizeMovers(), and setupMovers().

moves::TrialMoverOP protocols::surface_docking::FullatomRelaxMover::small_trial_min_mover_

private

Referenced by apply(), and FinalizeMovers().

std::string protocols::surface_docking::FullatomRelaxMover::smallmin_type_

private

Referenced by setup_defaults(), and setupMovers().

simple_moves::MinMoverOP protocols::surface_docking::FullatomRelaxMover::smallminmover_

private

Referenced by apply(), and setupMovers().

moves::MonteCarloOP protocols::surface_docking::FullatomRelaxMover::smallmonteCarlo_

private

Referenced by FinalizeMovers().

core::kinematics::MoveMapOP protocols::surface_docking::FullatomRelaxMover::smallmoveMapOP_

private

simple_moves::SmallMoverOP protocols::surface_docking::FullatomRelaxMover::smallmover_

private

Referenced by set_smallmovesize(), and setupMovers().

moves::SequenceMoverOP protocols::surface_docking::FullatomRelaxMover::smallsequenceMover_

private

Referenced by FinalizeMovers(), and setupMovers().

core::Real protocols::surface_docking::FullatomRelaxMover::temperature_

private

Referenced by FullatomRelaxMover(), and setupMovers().

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

• src/protocols/surface_docking/FullatomRelaxMover.hh
• src/protocols/surface_docking/FullatomRelaxMover.cc