#include <ThreadingMover.hh>

Inheritance diagram for protocols::comparative_modeling::ThreadingMover:

Collaboration diagram for protocols::comparative_modeling::ThreadingMover:

Public Member Functions
	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...

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

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
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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::TagPtr	TagPtr

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 38 of file ThreadingMover.hh.

Constructor & Destructor Documentation

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.

Definition at line 79 of file ThreadingMover.cc.

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

inlinevirtual

Definition at line 50 of file ThreadingMover.hh.

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.

Definition at line 107 of file ThreadingMover.cc.

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.

Definition at line 123 of file ThreadingMover.cc.

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.

Definition at line 253 of file ThreadingMover.cc.

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, core::conformation::Residue::clone(), core::pose::Pose::conformation(), protocols::loops::LoopMoverFactory::create_loop_mover(), frag_libs(), protocols::loops::LoopMoverFactory::get_instance(), get_qt_mapping(), core::scoring::getScoreFunction(), core::chemical::ResidueType::has(), core::chemical::ResidueType::has_atom_name(), core::conformation::idealize_hydrogens(), core::pose::initialize_atomid_map(), 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(), 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::chemical::ResidueType::residue_type_set(), core::sequence::SequenceAlignment::sequence(), core::pose::Pose::sequence(), core::pose::Pose::set_xyz(), 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)

Definition at line 132 of file ThreadingMover.cc.

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

Definition at line 145 of file ThreadingMover.cc.

References build_query_loops_.

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

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

Definition at line 165 of file ThreadingMover.cc.

References frag_libs_.

Referenced by apply().

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

Definition at line 169 of file ThreadingMover.cc.

References frag_libs_.

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.

Definition at line 443 of file ThreadingMover.cc.

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

Returns the SequenceMapping between query and template.

Definition at line 175 of file ThreadingMover.cc.

References align_, query_index_, core::sequence::SequenceAlignment::sequence(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), 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)

Definition at line 157 of file ThreadingMover.cc.

References min_loop_size_.

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

Definition at line 161 of file ThreadingMover.cc.

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.

Definition at line 96 of file ThreadingMover.cc.

References query_index_.

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

Sets the index of the query sequence in SequenceAlignment object.

Definition at line 112 of file ThreadingMover.cc.

References query_index_.

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

Definition at line 136 of file ThreadingMover.cc.

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 ( )

Definition at line 153 of file ThreadingMover.cc.

References randomize_loop_coords_.

Referenced by apply().

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

Definition at line 140 of file ThreadingMover.cc.

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

Definition at line 149 of file ThreadingMover.cc.

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.

Definition at line 102 of file ThreadingMover.cc.

References template_index_.

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

Sets the index of the template sequence in SequenceAlignment object.

Definition at line 118 of file ThreadingMover.cc.

References template_index_.

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

Definition at line 127 of file ThreadingMover.cc.

References template_pose_.

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

Member Data Documentation

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

private

Definition at line 125 of file ThreadingMover.hh.

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

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

private

Definition at line 132 of file ThreadingMover.hh.

bool protocols::comparative_modeling::ThreadingMover::build_query_loops_

private

Definition at line 126 of file ThreadingMover.hh.

Referenced by build_loops().

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

private

Definition at line 133 of file ThreadingMover.hh.

Referenced by frag_libs().

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

private

Definition at line 129 of file ThreadingMover.hh.

Referenced by min_loop_size().

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

private

Definition at line 123 of file ThreadingMover.hh.

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

bool protocols::comparative_modeling::ThreadingMover::randomize_loop_coords_

private

Definition at line 128 of file ThreadingMover.hh.

Referenced by randomize_loop_coords().

bool protocols::comparative_modeling::ThreadingMover::repack_query_

private

Definition at line 127 of file ThreadingMover.hh.

Referenced by repack_query().

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

private

Definition at line 123 of file ThreadingMover.hh.

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

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

private

Definition at line 124 of file ThreadingMover.hh.

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

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation