#include <MultiThreadingMover.hh>

Inheritance diagram for protocols::comparative_modeling::MultiThreadingMover:

Public Types
typedef core::sequence::SequenceAlignment	Alignment

typedef utility::vector1 < Alignment >	Alignments

typedef utility::vector1 < core::pose::Pose >	Poses

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

Public Member Functions
	MultiThreadingMover (Alignments const &aligns, Poses const &template_poses)
	align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model. More...

	~MultiThreadingMover () override=default

void	build_loops (bool setting)
	Returns the SequenceAlignments used in threading. More...

void	randomize_loop_coords (bool setting)

void	repack_query (bool setting)

bool	build_loops () const

bool	repack_query () const

bool	randomize_loop_coords ()

void	min_loop_size (core::Size const new_size)

core::Size	min_loop_size () const

utility::vector1 < core::fragment::FragSetOP >	frag_libs () const

void	frag_libs (utility::vector1< core::fragment::FragSetOP > new_libs)

void	apply (core::pose::Pose &query_pose) override
	Threads the given Pose onto the template_pose with the SequenceAlignment provided. More...

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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	check_internals () const

Private Attributes
Poses	template_poses_

Alignments	alignments_

bool	build_query_loops_

bool	repack_query_

bool	randomize_loop_coords_

core::Size	min_loop_size_

utility::vector1 < core::fragment::FragSetOP >	frag_libs_

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. 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::sequence::SequenceAlignment protocols::comparative_modeling::MultiThreadingMover::Alignment

typedef utility::vector1< Alignment > protocols::comparative_modeling::MultiThreadingMover::Alignments

typedef utility::vector1< core::pose::Pose > protocols::comparative_modeling::MultiThreadingMover::Poses

Constructor & Destructor Documentation

protocols::comparative_modeling::MultiThreadingMover::MultiThreadingMover	(	Alignments const &	aligns,
		Poses const &	template_poses
	)

align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model.

protocols::comparative_modeling::MultiThreadingMover::~MultiThreadingMover ( )

overridedefault

Member Function Documentation

void protocols::comparative_modeling::MultiThreadingMover::apply ( core::pose::Pose & query_pose )

overridevirtual

Threads the given Pose onto the template_pose with the SequenceAlignment provided.

Implements protocols::moves::Mover.

References alignments_, protocols::comparative_modeling::ThreadingMover::apply(), protocols::comparative_modeling::ThreadingMover::build_loops(), check_internals(), core::pose::initialize_atomid_map(), core::conformation::Residue::natoms(), protocols::comparative_modeling::ThreadingMover::randomize_loop_coords(), protocols::comparative_modeling::randomize_selected_atoms(), protocols::comparative_modeling::ThreadingMover::repack_query(), core::pose::Pose::residue(), core::sequence::SequenceAlignment::sequence_mapping(), core::pose::Pose::size(), and template_poses_.

void protocols::comparative_modeling::MultiThreadingMover::build_loops ( bool setting )

Returns the SequenceAlignments used in threading.

Manipulate the SequenceAlignments associated with this object.

References build_query_loops_.

bool protocols::comparative_modeling::MultiThreadingMover::build_loops ( ) const

References build_query_loops_.

void protocols::comparative_modeling::MultiThreadingMover::check_internals ( ) const

private

References alignments_, and template_poses_.

Referenced by apply().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::MultiThreadingMover::frag_libs ( ) const

References frag_libs_.

void protocols::comparative_modeling::MultiThreadingMover::frag_libs ( utility::vector1< core::fragment::FragSetOP > new_libs )

References frag_libs_.

std::string protocols::comparative_modeling::MultiThreadingMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::comparative_modeling::MultiThreadingMover::min_loop_size ( core::Size const new_size )

References min_loop_size_.

core::Size protocols::comparative_modeling::MultiThreadingMover::min_loop_size ( ) const

References min_loop_size_.

void protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords ( bool setting )

References randomize_loop_coords_.

bool protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords ( )

References randomize_loop_coords_.

void protocols::comparative_modeling::MultiThreadingMover::repack_query ( bool setting )

References repack_query_.

bool protocols::comparative_modeling::MultiThreadingMover::repack_query ( ) const

References repack_query_.

Member Data Documentation

Alignments protocols::comparative_modeling::MultiThreadingMover::alignments_

private

Referenced by apply(), and check_internals().

bool protocols::comparative_modeling::MultiThreadingMover::build_query_loops_

private

Referenced by build_loops().

utility::vector1< core::fragment::FragSetOP > protocols::comparative_modeling::MultiThreadingMover::frag_libs_

private

Referenced by frag_libs().

core::Size protocols::comparative_modeling::MultiThreadingMover::min_loop_size_

private

Referenced by min_loop_size().

bool protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords_

private

Referenced by randomize_loop_coords().

bool protocols::comparative_modeling::MultiThreadingMover::repack_query_

private

Referenced by repack_query().

Poses protocols::comparative_modeling::MultiThreadingMover::template_poses_

private

Referenced by apply(), and check_internals().

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

src/protocols/comparative_modeling/MultiThreadingMover.hh
src/protocols/comparative_modeling/MultiThreadingMover.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation