Build loops from scratch. More...

#include <LoopBuilder.hh>

Inheritance diagram for protocols::loop_modeling::LoopBuilder:

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

	~LoopBuilder () override
	Default destructor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Return the name of this mover. More...

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

core::Size	get_max_attempts () const
	Return the number of times KIC will be invoked before the LoopBuilder gives up. More...

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

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

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

utilities::TrajectoryLoggerOP	get_logger () const
	Return the object that report on the progress of the protocol. More...

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Configure from a RosettaScripts tag. More...

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

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

virtual void	get_children_names (utility::vector1< std::string > &names, std::string indent="") const
	Add the names of all the algorithms invoked by this loop mover to the given list. Indentation is used to represent hierarchy. More...

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

void	was_successful (bool value)
	Set the success status of a loop mover. More...

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

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

Loop const &	get_loop (core::Size index) const
	Return the specified loop. More...

void	set_loops (LoopsOP loops)
	Set the loops 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_loop (Loop const &loop)
	Set the loop to be sampled on the next call to apply(). More...

template<typename ToolTypeOP >
ToolTypeOP	get_tool (std::string key) const
	Request a tool from this mover or any of its parents. More...

template<typename ToolTypeOP >
ToolTypeOP	get_tool (std::string key, ToolTypeOP fallback) const
	Request a tool from this mover or any of its parents. More...

template<typename ToolTypeOP >
ToolTypeOP	set_tool (std::string key, ToolTypeOP value)
	Provide a tool for this mover or any of its children to use. 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, this mover will setup a fold tree on its own every time apply() is called. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	get_score_function_attributes (utility::tag::AttributeList &attlist)

Static Public Member Functions inherited from protocols::loop_modeling::LoopMover
static void	setup_fold_tree (Pose &pose, LoopsCOP loops, FoldTreeRequest request)
	Setup the given pose with a fold tree that is compatible with the given loops and requests. More...

static void	define_composition_schema (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen, utility::tag::XMLSchemaSimpleSubelementList &subelements)

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...

Protected Member Functions
bool	do_apply (Pose &pose, Loop const &loop) override
	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...

template<typename ChildSubclassOP >
ChildSubclassOP	add_child (ChildSubclassOP child)
	Add a child to this mover. More...

void	remove_child (LoopMoverOP child)
	Remove a child from this mover. More...

void	clear_children ()
	Remove all children from this mover. More...

LoopMoverOPs	get_children () const
	Return all of this mover's children. More...

core::Size	count_children () const
	Return the number of children this mover has. 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	idealize_loop (Pose &pose, Loop const &loop, core::kinematics::FoldTree &ft) const
	Idealize the loop with a give fold tree The fold tree of the pose is restored after the idealization. More...

Private Attributes
protocols::kinematic_closure::KicMoverOP	kic_mover_

refiners::MinimizationRefinerOP	minimizer_

utilities::TrajectoryLoggerOP	logger_

core::Size	max_attempts_

Friends
class	::LoopModelerTests

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 std::list< std::string >	Strings

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.

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

overridedefault

Default destructor.

Member Function Documentation

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

overrideprotectedvirtual

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

Reimplemented from protocols::loop_modeling::LoopMover.

References core::kinematics::FoldTree::add_edge(), protocols::loops::idealize_loop(), protocols::loops::Loop::is_extended(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

utilities::TrajectoryLoggerOP protocols::loop_modeling::LoopBuilder::get_logger ( ) const

Return the object that report on the progress of the protocol.

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

overridevirtual

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

Implements protocols::moves::Mover.

ScoreFunctionOP protocols::loop_modeling::LoopBuilder::get_score_function ( ) const

Get the score function to be used on the next call to apply().

void protocols::loop_modeling::LoopBuilder::get_score_function_attributes ( utility::tag::AttributeList & attlist )

static

References core::scoring::attributes_for_parse_score_function().

void protocols::loop_modeling::LoopBuilder::idealize_loop	(	Pose &	pose,
		Loop const &	loop,
		core::kinematics::FoldTree &	ft
	)		const

private

Idealize the loop with a give fold tree The fold tree of the pose is restored after the idealization.

References core::pose::Pose::fold_tree(), and protocols::loops::idealize_loop().

string protocols::loop_modeling::LoopBuilder::mover_name ( )

static

void protocols::loop_modeling::LoopBuilder::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Return the name of this mover.

Configure from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

References protocols::loop_modeling::utilities::set_scorefxn_from_tag().

void protocols::loop_modeling::LoopBuilder::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Specify how many time to invoke KIC before giving up.

void protocols::loop_modeling::LoopBuilder::set_score_function ( core::scoring::ScoreFunctionOP score_function )

Set the score function to be used on the next call to apply().

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

Use the given fragment libraries when building the loop.

Friends And Related Function Documentation

friend class ::LoopModelerTests

friend

Member Data Documentation

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

private

utilities::TrajectoryLoggerOP protocols::loop_modeling::LoopBuilder::logger_

private

core::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

Static Public Member Functions

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