Monte Carlo search for low energy loop conformations. More...

#include <LoopProtocol.hh>

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

	~LoopProtocol ()
	Default destructor. More...

string	get_name () const
	Return the class name of this mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	add_mover (LoopMoverOP mover)
	Add a LoopMover to the simulation. More...

void	add_refiner (LoopMoverOP refiner)
	Add a LoopMover to the simulation as a refiner. More...

void	add_filter (protocols::filters::FilterOP filter)
	Add a Filter to the simulation. More...

void	add_acceptance_check (string name="loop_move")
	Add an acceptance check to the simulation. More...

void	add_logger (loggers::LoggerOP logger)
	Add a logger to this simulation. More...

void	clear_movers ()

void	clear_refiners ()

void	clear_movers_and_refiners ()

void	mark_as_default ()

void	set_sfxn_cycles (Size x)
	Specify how many times the loop that ramps the score function should iterate. More...

void	set_temp_cycles (Size x, bool times_loop_length=false)
	Specify how many times the loop that ramps the temperature should iterate. More...

void	set_mover_cycles (Size x)
	Specify how many times the loops movers should be invoked after the score function and temperature have been updated. More...

void	set_temperature_schedule (Real start, Real stop)
	Set the initial and final temperatures for the simulation. More...

void	set_temperature_ramping (bool value)
	Enable or disable temperature ramping in this simulation. More...

void	set_repulsive_term_ramping (bool value)
	Enable or disable ramping the repulsive term of the score function. More...

void	set_rama_term_ramping (bool value)
	Enable or disable ramping the repulsive term of the score function. More...

Public Member Functions inherited from protocols::loop_modeling::LoopMover
	LoopMover ()
	Default constructor. More...

	~LoopMover ()
	Default destructor. More...

void	apply (Pose &pose)
	Sample the pose in the regions specified by get_loops(). More...

bool	was_successful () const
	Return true if the previous move was successful. More...

Loops	get_loops () const
	Return the loops to be sampled on the next call to apply(). More...

core::scoring::ScoreFunctionCOP	get_score_function () const
	Return the score function to be used on the next call to apply(). More...

core::scoring::ScoreFunctionOP	get_score_function ()
	Return the score function to be used on the next call to apply() (non-const access). More...

void	set_loop (Loop const &loop)
	Set the loop to be sampled on the next call to apply(). More...

void	set_loops (Loops const &loops)
	Set the loops to be sampled on the next call to apply(). More...

void	set_score_function (core::scoring::ScoreFunctionOP sfxn)
	Set the score function to be used on the next call to apply(). More...

virtual FoldTreeRequest	request_fold_tree () const
	Return an enum representing the kind of fold tree that is compatible with this mover. More...

void	trust_fold_tree ()
	Promise that the calling code will setup a fold tree compatible with request_fold_tree(). If this method is not called, most movers will setup a fold tree on their own the first time apply() is called. 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

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

Protected Member Functions
bool	do_apply (Pose &pose)
	Use a Monte Carlo simulation to search for the best conformations for the given loops. More...

Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool	do_apply (Pose &pose, Loop const &loop)
	Perform the loop sampling move. This method can be overwritten in child classes. More...

void	dont_manage_score_function ()
	Disable all the LoopMover score function related methods. More...

template<class LoopMoverSubclassOP >
LoopMoverSubclassOP	register_nested_loop_mover (LoopMoverSubclassOP mover)
	Indicate that the given loop mover is used within do_apply(). More...

void	deregister_nested_loop_movers ()
	Drop association with any currently registered loop movers. More...

vector1< LoopMoverOP > const &	get_nested_loop_movers () const
	Return a reference to the list of nested loop movers. 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	start_protocol (Pose &pose)
	Setup the aspects of the simulation like the loop movers, the score function, the fold tree, and the temperature. More...

void	ramp_temperature (Size iteration)
	Change the temperature of the simulation. This is called once every level-1 cycle. More...

void	ramp_score_function (Size iteration)
	Change the weights of the repulsive score function terms. This is called once every level-2 cycle. More...

void	attempt_loop_move (Pose &pose, Size i, Size j, Size k)
	Sample a new conformation by applying all the loop movers. Afterwards apply the Metropolis accept-or-reject criterion. This is called once every level-3 cycle. More...

void	finish_protocol (Pose &pose)
	Finalize any loggers and restore the original fold tree. 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::loop_modeling::LoopMover
static void	setup_fold_tree (Pose &pose, Loops const &loops, FoldTreeRequest request)
	Setup the given pose with a fold tree that is compatible with the given loops and requests. More...

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...

Detailed Description

Monte Carlo search for low energy loop conformations.

This class provides an easy way to run a Monte Carlo simulation searching for the lowest energy conformations for a set of loops. This is most common way to use the classes in this namespace. This simulation is organized into three nested loops. On each iteration of the outermost loop, the lowest scoring pose is recovered and the repulsive terms in the score function may be ramped (although this ramping is disabled by default). On each iteration of the intermediate loop, the temperature may be ramped (this ramping is enabled by default). And on each iteration of the innermost loop, a new conformation is sampled and either accepted or rejected according to the Metropolis criterion. The intermediate loop usually goes through more than 100 iterations, while the innermost and outermost loops only go through less than 5.

Like any mover, all the work is done by the apply() method. The rest of the methods of this class are just getters and setters that can be used to control various aspects of the simulation. The add_mover(), add_filter(), and add_acceptance_check() methods are worth drawing some attention to. These methods are used to build up the group of LoopMover objects that samples new loop conformations in the innermost loop. The movers are guaranteed to be applied in the order they are added to the protocol.

Constructor & Destructor Documentation

protocols::loop_modeling::LoopProtocol::LoopProtocol ( )

Default constructor.

protocols::loop_modeling::LoopProtocol::~LoopProtocol ( )

Default destructor.

Member Function Documentation

void protocols::loop_modeling::LoopProtocol::add_acceptance_check ( string name = "loop_move" )

Add an acceptance check to the simulation.

An acceptance check is always performed after all the loop movers have been applied, unless one of the movers failed. This method allows additional acceptance checks to be included in the protocol by adding a loop mover that does nothing but make that check.

void protocols::loop_modeling::LoopProtocol::add_filter ( protocols::filters::FilterOP filter )

Add a Filter to the simulation.

void protocols::loop_modeling::LoopProtocol::add_logger ( loggers::LoggerOP logger )

Add a logger to this simulation.

The Logger subclasses are only meant to be used with LoopProtocol. These classes do not derive from LoopMover, and implement a number of methods specifically designed for expressive logging output.

void protocols::loop_modeling::LoopProtocol::add_mover ( LoopMoverOP mover )

Add a LoopMover to the simulation.

Loop movers will be applied in the order they're added.

void protocols::loop_modeling::LoopProtocol::add_refiner ( LoopMoverOP refiner )

Add a LoopMover to the simulation as a refiner.

This method is very similar to add_mover(). Both methods add a new LoopMover to the simulation. This difference is subtle, but relevant when a LoopProtocol is being filled with a default set of movers that might be modified later.

This situation arises when a LoopModeler object is being constructed, or when a <LoopModeler> tag is being parsed by rosetta scripts. In both of these cases, centroid and fullatom LoopProtocols are created right away and filled with default movers. This avoids the necessity of specifying all the usual movers every time loop modeling is invoked. But the default movers may be subsequently overridden. In this case, there is a difference between LoopMovers added via add_mover() (i.e. movers) and add_refiner() (i.e. refiners).

The difference is that movers can be marked as "default" and then be implicitly overridden. Consider the following sequence of calls:

protocol->add_mover(new CcdMover);
protocol->mark_as_default();
protocol->add_mover(new KicMover);

This will result in a LoopProtocol containing only a KicMover. When mark_as_default() is called, all movers within the protocol are set to be replaced the next time add_mover() is called. You can think of those movers as being part of a default configuration that should be replaced when a new configuration is given.

Refiners are not affected by mark_as_default(). Calling add_refiner() will always add a refiner and will never remove old ones, although old refiners can be explicitly removed with clear_refiners(). Refiners are also applied after movers, regardless of the order in which add_mover() and add_refiner() were called. The purpose of all this is to make it easy to replace the parts of a LoopProtocol that are more variable without having to also replace those that are more static.

The variable part of a LoopProtocol is typically the sampling algorithm: KIC or CCD, often with myriad options. The static part is typically the refinement algorithm: minimization, rotamer trials, and repacking, all with carefully tuned parameters. Using add_mover(), mark_as_default(), and add_refiner() makes it easy to change the sampling algorithm without having to worry about the refinement algorithm.

void protocols::loop_modeling::LoopProtocol::attempt_loop_move	(	Pose &	pose,
		Size	i,
		Size	j,
		Size	k
	)

private

Sample a new conformation by applying all the loop movers. Afterwards apply the Metropolis accept-or-reject criterion. This is called once every level-3 cycle.

void protocols::loop_modeling::LoopProtocol::clear_movers ( )

void protocols::loop_modeling::LoopProtocol::clear_movers_and_refiners ( )

void protocols::loop_modeling::LoopProtocol::clear_refiners ( )

bool protocols::loop_modeling::LoopProtocol::do_apply ( Pose & pose )

protectedvirtual

Use a Monte Carlo simulation to search for the best conformations for the given loops.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopProtocol::finish_protocol ( Pose & pose )

private

Finalize any loggers and restore the original fold tree.

string protocols::loop_modeling::LoopProtocol::get_name ( ) const

inlinevirtual

Return the class name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopProtocol::mark_as_default ( )

void protocols::loop_modeling::LoopProtocol::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References cycles, loop_mover, protocols::loop_modeling::utilities::loop_mover_from_tag(), s1, and s2.

void protocols::loop_modeling::LoopProtocol::ramp_score_function ( Size iteration )

private

Change the weights of the repulsive score function terms. This is called once every level-2 cycle.

References core::scoring::fa_rep, fa_rep, get_score_function(), core::scoring::rama, and rama.

void protocols::loop_modeling::LoopProtocol::ramp_temperature ( Size iteration )

private

Change the temperature of the simulation. This is called once every level-1 cycle.

References temperature.

void protocols::loop_modeling::LoopProtocol::set_mover_cycles ( Size x )

Specify how many times the loops movers should be invoked after the score function and temperature have been updated.

The mover loop is the innermost loop. It is contained by the score function loop and the temperature loop.

void protocols::loop_modeling::LoopProtocol::set_rama_term_ramping ( bool value )

Enable or disable ramping the repulsive term of the score function.

void protocols::loop_modeling::LoopProtocol::set_repulsive_term_ramping ( bool value )

Enable or disable ramping the repulsive term of the score function.

void protocols::loop_modeling::LoopProtocol::set_sfxn_cycles ( Size x )

Specify how many times the loop that ramps the score function should iterate.

The score function loop is the outermost loop. It contains the temperature loop and the mover loop.

void protocols::loop_modeling::LoopProtocol::set_temp_cycles	(	Size	x,
		bool	times_loop_length = `false`
	)

Specify how many times the loop that ramps the temperature should iterate.

The temperature loop is contained by the score function loop. It contains the mover loop.

void protocols::loop_modeling::LoopProtocol::set_temperature_ramping ( bool value )

Enable or disable temperature ramping in this simulation.

void protocols::loop_modeling::LoopProtocol::set_temperature_schedule	(	Real	start,
		Real	stop
	)

Set the initial and final temperatures for the simulation.

The temperature will be linearly interpolated between these values during the simulation.

References protocols::loops::start, and protocols::loops::stop.

void protocols::loop_modeling::LoopProtocol::start_protocol ( Pose & pose )

private

Setup the aspects of the simulation like the loop movers, the score function, the fold tree, and the temperature.

References protocols::loops::add_cutpoint_variants(), get_score_function(), protocols::loops::loop_mover::loops_set_chainbreak_weight(), make_vector1(), and utility_exit_with_message.

Member Data Documentation

Real protocols::loop_modeling::LoopProtocol::final_temp_

private

Real protocols::loop_modeling::LoopProtocol::initial_temp_

private

loggers::LoggerList protocols::loop_modeling::LoopProtocol::loggers_

private

protocols::moves::MonteCarloOP protocols::loop_modeling::LoopProtocol::monte_carlo_

private

Size protocols::loop_modeling::LoopProtocol::mover_cycles_

private

utilities::LoopMoverGroupOP protocols::loop_modeling::LoopProtocol::movers_

private

core::kinematics::FoldTree protocols::loop_modeling::LoopProtocol::original_tree_

private

utilities::LoopMoverGroupOP protocols::loop_modeling::LoopProtocol::protocol_

private

bool protocols::loop_modeling::LoopProtocol::ramp_sfxn_rama_

private

bool protocols::loop_modeling::LoopProtocol::ramp_sfxn_rep_

private

bool protocols::loop_modeling::LoopProtocol::ramp_temp_

private

utilities::LoopMoverGroupOP protocols::loop_modeling::LoopProtocol::refiners_

private

bool protocols::loop_modeling::LoopProtocol::scale_temp_cycles_

private

Size protocols::loop_modeling::LoopProtocol::sfxn_cycles_

private

Size protocols::loop_modeling::LoopProtocol::temp_cycles_

private

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

src/protocols/loop_modeling/LoopProtocol.hh
src/protocols/loop_modeling/LoopProtocol.cc

Private Attributes
utilities::LoopMoverGroupOP	protocol_

utilities::LoopMoverGroupOP	movers_

utilities::LoopMoverGroupOP	refiners_

protocols::moves::MonteCarloOP	monte_carlo_

core::kinematics::FoldTree	original_tree_

loggers::LoggerList	loggers_

Size	sfxn_cycles_

Size	temp_cycles_

Size	mover_cycles_

bool	ramp_sfxn_rep_

bool	ramp_sfxn_rama_

bool	ramp_temp_

bool	scale_temp_cycles_

Real	initial_temp_

Real	final_temp_

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation