#include <ThreadingMover.hh>

Public Member Functions
	ThreadingMover ()
	Empty constructor. More...

	ThreadingMover (ThreadingMover const &object_to_copy)
	Copy constructor. More...

	ThreadingMover (core::sequence::SequenceAlignment const &align, core::pose::Pose const &template_pose)
	align describes the association between the query and template sequences, template_pose is the conformation from which to build a threading model. More...

virtual	~ThreadingMover ()

core::Size	query_index () const
	Returns the index of the query sequence in SequenceAlignment object. More...

core::Size	template_index () const
	Returns the index of the template sequence in SequenceAlignment object. More...

core::sequence::SequenceAlignment	alignment ()
	Returns the SequenceAlignment object used in threading. More...

void	query_index (core::Size new_index)
	Sets the index of the query sequence in SequenceAlignment object. More...

void	template_index (core::Size new_index)
	Sets the index of the template sequence in SequenceAlignment object. More...

void	alignment (core::sequence::SequenceAlignment new_align)
	Sets the SequenceAlignment associated with this object. More...

void	template_pose (core::pose::Pose template_pose)

void	build_loops (bool setting)

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)

Size	min_loop_size () const

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

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

core::id::SequenceMapping	get_qt_mapping (core::pose::Pose const &query_pose) const
	Returns the SequenceMapping between query and template. More...

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

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

virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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 void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...

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...

Private Member Functions
bool	atoms_are_equiv (std::string const &a1, std::string const &a2)

void	add_equiv_atoms (std::string const &a1, std::string const &a2)
	add pair of equivalent atoms to atom_equiv_ table. More...

void	init_atom_equiv ()
	initialize table of equivalent atoms between all residues. More...

Private Attributes
core::Size	query_index_

core::Size	template_index_

core::pose::Pose	template_pose_

core::sequence::SequenceAlignment	align_

bool	build_query_loops_

bool	repack_query_

bool	randomize_loop_coords_

core::Size	min_loop_size_

std::map< std::string, std::set< std::string > >	atom_equiv_

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

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::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...

Constructor & Destructor Documentation

protocols::comparative_modeling::ThreadingMover::ThreadingMover ( )

Empty constructor.

Referenced by clone(), and fresh_instance().

protocols::comparative_modeling::ThreadingMover::ThreadingMover ( ThreadingMover const & object_to_copy )

Copy constructor.

protocols::comparative_modeling::ThreadingMover::ThreadingMover	(	core::sequence::SequenceAlignment const &	align,
		core::pose::Pose const &	template_pose
	)

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

virtual protocols::comparative_modeling::ThreadingMover::~ThreadingMover ( )

inlinevirtual

Member Function Documentation

void protocols::comparative_modeling::ThreadingMover::add_equiv_atoms	(	std::string const &	a1,
		std::string const &	a2
	)

private

add pair of equivalent atoms to atom_equiv_ table.

core::sequence::SequenceAlignment protocols::comparative_modeling::ThreadingMover::alignment ( )

Returns the SequenceAlignment object used in threading.

References align_.

Referenced by protocols::comparative_modeling::PartialThreadingMover::parse_my_tag().

void protocols::comparative_modeling::ThreadingMover::alignment ( core::sequence::SequenceAlignment new_align )

Sets the SequenceAlignment associated with this object.

References align_.

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::comparative_modeling::PartialThreadingMover.

References core::pose::add_score_line_string(), align_, core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_name(), build_loops(), core::chemical::CENTROID, protocols::loops::Loops::choose_cutpoints(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), protocols::loops::LoopMoverFactory::create_loop_mover(), utility::file_basename(), frag_libs(), protocols::loops::LoopMoverFactory::get_instance(), get_qt_mapping(), get_score_function(), core::chemical::ResidueType::has(), core::conformation::idealize_hydrogens(), core::pose::initialize_atomid_map(), cm::loop_mover, loop_mover, protocols::comparative_modeling::loops_from_alignment(), min_loop_size(), core::chemical::ResidueTypeSet::name(), core::conformation::Residue::name1(), core::conformation::Residue::natoms(), core::pack::optimize_H_and_notify(), option, core::pack::pack_missing_sidechains(), core::pose::Pose::pdb_info(), core::scoring::peptide_bond, query_index_, randomize_loop_coords(), protocols::comparative_modeling::randomize_selected_atoms(), repack_query(), core::pose::Pose::replace_residue(), resi, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::sequence::SequenceAlignment::sequence(), core::pose::Pose::sequence(), core::pose::Pose::set_xyz(), protocols::loops::Loops::size(), core::util::switch_to_residue_type_set(), template_index_, template_pose_, core::pose::Pose::total_residue(), protocols::comparative_modeling::tr, and core::pose::Pose::xyz().

Referenced by protocols::domain_assembly::CombineChainsMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

bool protocols::comparative_modeling::ThreadingMover::atoms_are_equiv	(	std::string const &	a1,
		std::string const &	a2
	)

private

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

References build_query_loops_.

Referenced by protocols::domain_assembly::CombineChainsMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

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

References build_query_loops_.

Referenced by protocols::comparative_modeling::PartialThreadingMover::apply(), and apply().

protocols::moves::MoverOP protocols::comparative_modeling::ThreadingMover::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References ThreadingMover().

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

References frag_libs_.

Referenced by apply().

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

References frag_libs_.

protocols::moves::MoverOP protocols::comparative_modeling::ThreadingMover::fresh_instance ( ) const

virtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ThreadingMover().

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::comparative_modeling::PartialThreadingMover.

core::id::SequenceMapping protocols::comparative_modeling::ThreadingMover::get_qt_mapping ( core::pose::Pose const & query_pose ) const

Returns the SequenceMapping between query and template.

References align_, query_index_, core::sequence::SequenceAlignment::sequence(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), ss, template_index_, template_pose_, protocols::comparative_modeling::tr, and core::sequence::transitive_map().

Referenced by protocols::comparative_modeling::PartialThreadingMover::apply(), and apply().

void protocols::comparative_modeling::ThreadingMover::init_atom_equiv ( )

private

initialize table of equivalent atoms between all residues.

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

References min_loop_size_.

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

References min_loop_size_.

Referenced by apply().

core::Size protocols::comparative_modeling::ThreadingMover::query_index ( ) const

Returns the index of the query sequence in SequenceAlignment object.

References query_index_.

void protocols::comparative_modeling::ThreadingMover::query_index ( core::Size new_index )

Sets the index of the query sequence in SequenceAlignment object.

References query_index_.

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

References randomize_loop_coords_.

Referenced by protocols::domain_assembly::CombineChainsMover::apply(), protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords ( )

References randomize_loop_coords_.

Referenced by apply().

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

References repack_query_.

Referenced by protocols::comparative_modeling::MultiThreadingMover::apply(), and protocols::comparative_modeling::ThreadingJobInputter::pose_from_job().

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

References repack_query_.

Referenced by protocols::comparative_modeling::PartialThreadingMover::apply(), and apply().

core::Size protocols::comparative_modeling::ThreadingMover::template_index ( ) const

Returns the index of the template sequence in SequenceAlignment object.

References template_index_.

void protocols::comparative_modeling::ThreadingMover::template_index ( core::Size new_index )

Sets the index of the template sequence in SequenceAlignment object.

References template_index_.

void protocols::comparative_modeling::ThreadingMover::template_pose ( core::pose::Pose template_pose )

References template_pose_.

Referenced by protocols::comparative_modeling::PartialThreadingMover::parse_my_tag().

Member Data Documentation

core::sequence::SequenceAlignment protocols::comparative_modeling::ThreadingMover::align_

private

Referenced by alignment(), apply(), and get_qt_mapping().

std::map< std::string, std::set< std::string > > protocols::comparative_modeling::ThreadingMover::atom_equiv_

private

bool protocols::comparative_modeling::ThreadingMover::build_query_loops_

private

Referenced by build_loops().

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

private

Referenced by frag_libs().

core::Size protocols::comparative_modeling::ThreadingMover::min_loop_size_

private

Referenced by min_loop_size().

core::Size protocols::comparative_modeling::ThreadingMover::query_index_

private

Referenced by apply(), get_qt_mapping(), and query_index().

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords_

private

Referenced by randomize_loop_coords().

bool protocols::comparative_modeling::ThreadingMover::repack_query_

private

Referenced by repack_query().

core::Size protocols::comparative_modeling::ThreadingMover::template_index_

private

Referenced by apply(), get_qt_mapping(), and template_index().

core::pose::Pose protocols::comparative_modeling::ThreadingMover::template_pose_

private

Referenced by apply(), get_qt_mapping(), and template_pose().

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

src/protocols/comparative_modeling/ThreadingMover.hh
src/protocols/comparative_modeling/ThreadingMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation