#include <ChunkTrialMover.hh>

Public Member Functions
	ChunkTrialMover (utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, Loops ss_chunks_pose, bool random_template=true, AlignOption align_option=all_chunks, Size max_registry_shift=0)

	ChunkTrialMover (utility::vector1< core::pose::PoseCOP > const &template_poses, utility::vector1< protocols::loops::Loops > const &template_chunks, Loops ss_chunks_pose, bool random_template, AlignOption align_option, utility::vector1< bool > residue_sample_template, utility::vector1< Size > residue_max_registry_shift)

void	get_alignment_from_template (core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > &seqpos_alignment)

void	get_alignment_from_chunk_mapping (std::map< core::Size, core::Size > const &chunk_mapping, Loops const template_ss_chunks, Loops const target_ss_chunks, std::map< core::Size, core::Size > &sequence_alignment)

void	set_template (core::Size const template_number)

core::Size	template_number ()

void	pick_random_template ()

void	pick_random_chunk (core::pose::Pose &pose)

Size	trial_counter (Size ires)

void	apply (core::pose::Pose &pose)

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

void	set_templates_to_ignore (std::set< core::Size > template_indices_in)

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
	Return a clone of the Mover object. More...

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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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...

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::hybridization::ChunkTrialMover::ChunkTrialMover	(	utility::vector1< core::pose::PoseCOP > const &	template_poses,
		utility::vector1< protocols::loops::Loops > const &	template_chunks,
		Loops	ss_chunks_pose,
		bool	random_template = `true`,
		AlignOption	align_option = `all_chunks`,
		Size	max_registry_shift = `0`
	)

References cm::hybridize::alignment_from_chunk_mapping, cm::hybridize::alignment_from_template_seqpos, get_alignment_from_chunk_mapping(), get_alignment_from_template(), highest_tmpl_resnum_, option, residue_covered_by_template_, sequence_alignments_, size(), template_chunks_, template_poses_, protocols::moves::Mover::type(), user, and utility_exit_with_message.

protocols::hybridization::ChunkTrialMover::ChunkTrialMover	(	utility::vector1< core::pose::PoseCOP > const &	template_poses,
		utility::vector1< protocols::loops::Loops > const &	template_chunks,
		Loops	ss_chunks_pose,
		bool	random_template,
		AlignOption	align_option,
		utility::vector1< bool >	residue_sample_template,
		utility::vector1< Size >	residue_max_registry_shift
	)

References cm::hybridize::alignment_from_chunk_mapping, cm::hybridize::alignment_from_template_seqpos, get_alignment_from_chunk_mapping(), get_alignment_from_template(), highest_tmpl_resnum_, option, residue_max_registry_shift_, sampling_chunk_, sequence_alignments_, size(), template_chunks_, template_poses_, protocols::moves::Mover::type(), user, and utility_exit_with_message.

Member Function Documentation

void protocols::hybridization::ChunkTrialMover::apply ( core::pose::Pose & pose )

virtual

void protocols::hybridization::ChunkTrialMover::get_alignment_from_chunk_mapping	(	std::map< core::Size, core::Size > const &	chunk_mapping,
		Loops const	template_ss_chunks,
		Loops const	target_ss_chunks,
		std::map< core::Size, core::Size > &	sequence_alignment
	)

References length, max_registry_shift_global_, residue_max_registry_shift_, protocols::loops::Loops::size(), and protocols::loops::start.

Referenced by ChunkTrialMover().

void protocols::hybridization::ChunkTrialMover::get_alignment_from_template	(	core::pose::PoseCOP	template_pose,
		std::map< core::Size, core::Size > &	seqpos_alignment
	)

References protocols::hybridization::TR.

Referenced by ChunkTrialMover().

std::string protocols::hybridization::ChunkTrialMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::ChunkTrialMover::pick_random_chunk ( core::pose::Pose & pose )

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::downstream_jump_residue(), protocols::hybridization::downstream_residues_from_jump(), core::pose::Pose::fold_tree(), highest_tmpl_resnum_, jump_number_, ntrials, core::pose::Pose::num_jump(), numeric::random::RandomGenerator::random_range(), core::pose::Pose::residue(), protocols::hybridization::RG, and sampling_chunk_.

Referenced by apply().

void protocols::hybridization::ChunkTrialMover::pick_random_template ( )

References ignore_template_indices_, ntrials, numeric::random::RandomGenerator::random_range(), protocols::hybridization::RG, set_template(), size(), template_chunks_, template_number(), template_poses_, and utility_exit_with_message.

Referenced by apply().

void protocols::hybridization::ChunkTrialMover::set_template ( core::Size const template_number )

References template_number(), and template_number_.

Referenced by protocols::hybridization::FoldTreeHybridize::apply(), and pick_random_template().

void protocols::hybridization::ChunkTrialMover::set_templates_to_ignore ( std::set< core::Size > template_indices_in )

inline

core::Size protocols::hybridization::ChunkTrialMover::template_number ( )

References template_number_.

Referenced by apply(), pick_random_template(), and set_template().

Size protocols::hybridization::ChunkTrialMover::trial_counter ( Size ires )

References align_chunk_, and protocols::hybridization::InsertChunkMover::trial_counter().

Member Data Documentation

InsertChunkMover protocols::hybridization::ChunkTrialMover::align_chunk_

private

Referenced by apply(), and trial_counter().

AlignOption protocols::hybridization::ChunkTrialMover::align_option_

private

Referenced by apply().

Size protocols::hybridization::ChunkTrialMover::highest_tmpl_resnum_

private

Referenced by ChunkTrialMover(), and pick_random_chunk().

std::set< core::Size > protocols::hybridization::ChunkTrialMover::ignore_template_indices_

private

Referenced by apply(), and pick_random_template().

Size protocols::hybridization::ChunkTrialMover::jump_number_

private

Referenced by apply(), and pick_random_chunk().

Size protocols::hybridization::ChunkTrialMover::max_registry_shift_global_

private

Referenced by get_alignment_from_chunk_mapping().

bool protocols::hybridization::ChunkTrialMover::random_template_

private

Referenced by apply().

utility::vector1< core::Size > protocols::hybridization::ChunkTrialMover::residue_covered_by_template_

private

Referenced by apply(), and ChunkTrialMover().

utility::vector1< Size > protocols::hybridization::ChunkTrialMover::residue_max_registry_shift_

private

Referenced by ChunkTrialMover(), and get_alignment_from_chunk_mapping().

utility::vector1<bool> protocols::hybridization::ChunkTrialMover::sampling_chunk_

private

Referenced by ChunkTrialMover(), and pick_random_chunk().

utility::vector1< std::map <core::Size, core::Size> > protocols::hybridization::ChunkTrialMover::sequence_alignments_

private

Referenced by apply(), and ChunkTrialMover().

utility::vector1< Loops > protocols::hybridization::ChunkTrialMover::template_chunks_

private

Referenced by ChunkTrialMover(), and pick_random_template().

Size protocols::hybridization::ChunkTrialMover::template_number_

private

Referenced by set_template(), and template_number().

utility::vector1< core::pose::PoseCOP > protocols::hybridization::ChunkTrialMover::template_poses_

private

Referenced by apply(), ChunkTrialMover(), and pick_random_template().

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

symlinks/rosetta/src/protocols/hybridization/ChunkTrialMover.hh
symlinks/rosetta/src/protocols/hybridization/ChunkTrialMover.cc

Private Attributes
utility::vector1 < core::pose::PoseCOP >	template_poses_

utility::vector1< Loops >	template_chunks_

bool	random_template_

AlignOption	align_option_

InsertChunkMover	align_chunk_

utility::vector1< std::map < core::Size, core::Size > >	sequence_alignments_

utility::vector1< core::Size >	residue_covered_by_template_

Size	template_number_

Size	jump_number_

Size	highest_tmpl_resnum_

std::set< core::Size >	ignore_template_indices_

utility::vector1< bool >	sampling_chunk_

Size	max_registry_shift_global_

utility::vector1< Size >	residue_max_registry_shift_

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation