#include <ThreadingMover.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingMover:

[legend]

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...

	~ThreadingMover () override=default

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)

core::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...

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...

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. 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 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...

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
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 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

◆ ThreadingMover() [1/3]

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

Empty constructor.

◆ ThreadingMover() [2/3]

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

Copy constructor.

◆ ThreadingMover() [3/3]

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.

◆ ~ThreadingMover()

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

overridedefault

Member Function Documentation

◆ add_equiv_atoms()

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.

◆ alignment() [1/2]

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

Returns the SequenceAlignment object used in threading.

References align_.

◆ alignment() [2/2]

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

Sets the SequenceAlignment associated with this object.

References align_.

◆ apply()

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

overridevirtual

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

Implements protocols::moves::Mover.

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_t, core::conformation::Residue::clone(), core::pose::Pose::conformation(), frag_libs(), get_qt_mapping(), core::scoring::get_score_function(), core::chemical::ResidueType::has(), core::conformation::idealize_hydrogens(), core::pose::initialize_atomid_map(), protocols::comparative_modeling::loops_from_alignment(), min_loop_size(), core::conformation::Residue::name1(), core::pack::optimize_H_and_notify(), 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(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Conformation::residue_typeset_mode(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence(), core::pose::Pose::set_xyz(), core::id::SequenceMapping::show(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), template_index_, template_pose_, protocols::comparative_modeling::tr(), and core::pose::Pose::xyz().

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

◆ atoms_are_equiv()

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

private

◆ build_loops() [1/2]

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

References build_query_loops_.

Referenced by apply().

◆ build_loops() [2/2]

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().

◆ clone()

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

overridevirtual

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.

◆ frag_libs() [1/2]

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

References frag_libs_.

Referenced by apply().

◆ frag_libs() [2/2]

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

References frag_libs_.

◆ fresh_instance()

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

overridevirtual

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.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_qt_mapping()

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_, protocols::comparative_modeling::get_qt_mapping_general(), query_index_, template_index_, and template_pose_.

Referenced by apply().

◆ init_atom_equiv()

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

private

initialize table of equivalent atoms between all residues.

◆ min_loop_size() [1/2]

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

References min_loop_size_.

Referenced by apply().

◆ min_loop_size() [2/2]

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

References min_loop_size_.

◆ query_index() [1/2]

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

Returns the index of the query sequence in SequenceAlignment object.

References query_index_.

◆ query_index() [2/2]

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

Sets the index of the query sequence in SequenceAlignment object.

References query_index_.

◆ randomize_loop_coords() [1/2]

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

References randomize_loop_coords_.

Referenced by apply().

◆ randomize_loop_coords() [2/2]

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().

◆ repack_query() [1/2]

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

References repack_query_.

Referenced by apply().

◆ repack_query() [2/2]

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().

◆ template_index() [1/2]

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

Returns the index of the template sequence in SequenceAlignment object.

References template_index_.

◆ template_index() [2/2]

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

Sets the index of the template sequence in SequenceAlignment object.

References template_index_.

◆ template_pose()

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

References template_pose_.

Member Data Documentation

◆ align_

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

private

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

◆ atom_equiv_

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

private

◆ build_query_loops_

bool protocols::comparative_modeling::ThreadingMover::build_query_loops_

private

Referenced by build_loops().

◆ frag_libs_

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

private

Referenced by frag_libs().

◆ min_loop_size_

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

private

Referenced by min_loop_size().

◆ query_index_

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

private

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

◆ randomize_loop_coords_

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords_

private

Referenced by randomize_loop_coords().

◆ repack_query_

bool protocols::comparative_modeling::ThreadingMover::repack_query_

private

Referenced by repack_query().

◆ template_index_

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

private

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

◆ template_pose_

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

◆ ThreadingMover() [1/3]

◆ ThreadingMover() [2/3]

◆ ThreadingMover() [3/3]

◆ ~ThreadingMover()

Member Function Documentation

◆ add_equiv_atoms()

◆ alignment() [1/2]

◆ alignment() [2/2]

◆ apply()

◆ atoms_are_equiv()

◆ build_loops() [1/2]

◆ build_loops() [2/2]

◆ clone()

◆ frag_libs() [1/2]

◆ frag_libs() [2/2]

◆ fresh_instance()

◆ get_name()

◆ get_qt_mapping()

◆ init_atom_equiv()

◆ min_loop_size() [1/2]

◆ min_loop_size() [2/2]

◆ query_index() [1/2]

◆ query_index() [2/2]

◆ randomize_loop_coords() [1/2]

◆ randomize_loop_coords() [2/2]

◆ repack_query() [1/2]

◆ repack_query() [2/2]

◆ template_index() [1/2]

◆ template_index() [2/2]

◆ template_pose()

Member Data Documentation

◆ align_

◆ atom_equiv_

◆ build_query_loops_

◆ frag_libs_

◆ min_loop_size_

◆ query_index_

◆ randomize_loop_coords_

◆ repack_query_

◆ template_index_

◆ template_pose_