Build loops from scratch. More...

#include <LoopBuilder.hh>

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

string	get_name () const
	Return the 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)
	Configure from a RosettaScripts tag. More...

void	use_fragments (utility::vector1< core::fragment::FragSetCOP > const &frag_libs)
	Use the given fragment libraries when building the loop. More...

void	set_max_attempts (Size attempts)
	Specify how many time to invoke KIC before giving up. More...

Size	get_max_attempts () const
	Return the number of times KIC will be invoked before the LoopBuilder gives up. 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, Loop const &loop)
	Attempt to find a reasonable loop conformation without using any information from the original coordinates. More...

Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool	do_apply (Pose &pose)
	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 Attributes
protocols::kinematic_closure::KicMoverOP	kic_mover_

refiners::MinimizationRefinerOP	minimizer_

Size	max_attempts_

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

Build loops from scratch.

Author: Kale Kundert; Roland A. Pache, PhD

Building a loop from scratch is useful in two scenarios. The first is when there's missing density that needs to be modeled, and the second is when the whole loop modeling algorithm needs to be benchmarked. This mover uses kinematic closure (KIC) to build loops. By default, the loop are built by picking phi and psi values from a Ramachandran distribution and setting all other DOFs to ideal values. Phi and psi values can also be picked using fragment libraries. Loop building succeeds when a model is found that passes a more-lenient-than-usual bump check. If no such model is found after 1000 iterations, the mover gives up and reports failure.

This process can be very slow for long loops, because there's nothing guiding the algorithm towards the right solution. By default, torsions are just being randomly picked, and they often won't fit in the relatively narrow space that's available. The problem is worse for interior loops than it is for surface loops, of course. This algorithm seems to work well enough on 12 residue loops, but beyond that it may be necessary to develop a smarter algorithm that preferentially builds into free space.

Constructor & Destructor Documentation

protocols::loop_modeling::LoopBuilder::LoopBuilder ( )

Default constructor.

References option.

Member Function Documentation

bool protocols::loop_modeling::LoopBuilder::do_apply	(	Pose &	pose,
		Loop const &	loop
	)

protectedvirtual

Attempt to find a reasonable loop conformation without using any information from the original coordinates.

Reimplemented from protocols::loop_modeling::LoopMover.

References protocols::loops::Loop::is_extended(), and tr.

Size protocols::loop_modeling::LoopBuilder::get_max_attempts ( ) const

Return the number of times KIC will be invoked before the LoopBuilder gives up.

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

inlinevirtual

Return the name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopBuilder::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

Configure from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

void protocols::loop_modeling::LoopBuilder::set_max_attempts ( Size attempts )

Specify how many time to invoke KIC before giving up.

void protocols::loop_modeling::LoopBuilder::use_fragments ( utility::vector1< core::fragment::FragSetCOP > const & frag_libs )

Use the given fragment libraries when building the loop.

Member Data Documentation

protocols::kinematic_closure::KicMoverOP protocols::loop_modeling::LoopBuilder::kic_mover_

private

Size protocols::loop_modeling::LoopBuilder::max_attempts_

private

refiners::MinimizationRefinerOP protocols::loop_modeling::LoopBuilder::minimizer_

private

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

src/protocols/loop_modeling/LoopBuilder.hh
src/protocols/loop_modeling/LoopBuilder.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation