A FragmentMover that applies uniform sampling of fragments. More...

#include <FragmentMover.hh>

Inheritance diagram for protocols::simple_moves::ClassicFragmentMover:

Collaboration diagram for protocols::simple_moves::ClassicFragmentMover:

Public Member Functions
	ClassicFragmentMover (core::fragment::FragSetCOP fragset)

	ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)

	ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap)
	Temp work around for PyRosetta code, until we found a way how to handle owning pointers in this case More...

	~ClassicFragmentMover ()

void	apply (core::pose::Pose &)
	Applies classic fragment insertion based on a FragSet. More...

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

void	set_check_ss (bool setting)
	check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2) More...

bool	check_ss () const
	accessor More...

core::Real	end_bias () const

void	set_end_bias (core::Real setting)

bool	end_bias_check_enabled () const

void	enable_end_bias_check (bool setting=true)

void	set_min_overlap (Size setting)
	min_overlap controls the behaviour fragset->region() More...

void	set_min_frag_length (Size setting)
	min_frag_length controls the behaviour fragset->region() More...

virtual bool	apply_fragment (core::fragment::Frame const &frame, Size frag_num, core::kinematics::MoveMap const &movemap, core::pose::Pose &pose) const
	apply the chosen fragment, this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards More...

virtual void	set_defaults ()
	set defaults More...

virtual bool	choose_fragment (core::fragment::FrameList const &, core::pose::Pose const &, Size &frame_num, Size &frag_num) const
	given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found More...

void	define_start_window (Size window_start)
	apply fragment at predefined position More...

virtual bool	choose_window_start (core::pose::Pose const &, Size window_length, Size &window_start) const
	yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found ) More...

virtual bool	choose_window_length (core::pose::Pose const &, Size &window_length) const
	yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found ) More...

void	on_new_fragments ()
	is called from set_fragments() More...

virtual bool	end_bias_check (core::pose::Pose const &, Size window_start) const

virtual bool	valid_ss (std::string const &new_ss) const
	returns true if the ss string is acceptable More...

Public Member Functions inherited from protocols::simple_moves::FragmentMover
	~FragmentMover ()

virtual bool	apply (core::pose::Pose &, Size pos) const
	apply a fragment at pos to movemable dofs More...

virtual Size	apply_at_all_positions (core::pose::Pose &) const
	apply at all movemable positions — honors movemap More...

core::fragment::FragSetCOP	fragments () const
	accessor to the fragment set More...

virtual void	set_fragments (core::fragment::FragSetCOP new_frags_)
	setter for the fragment set More...

virtual void	set_movemap (core::kinematics::MoveMapCOP movemap)
	setter for the movemap More...

core::kinematics::MoveMapCOP	movemap () const

core::fragment::InsertMap const &	insert_map () const

core::fragment::InsertSize const &	insert_size () const

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

Protected Member Functions
	ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
	alternative Constructor to be used by derived classes More...

	ClassicFragmentMover (core::fragment::FragSetCOP fragset, std::string type)
	alternative Constructor to be used by derived classes More...

virtual bool	apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const

Protected Member Functions inherited from protocols::simple_moves::FragmentMover
	FragmentMover (core::fragment::FragSetCOP fragset, std::string type)

	FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
	constructor More...

void	update_insert_map ()

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...

Private Attributes
Size	min_overlap_

Size	min_frag_length_

bool	check_ss_

core::Real	end_bias_

bool	bApplyEndBias_

bool	use_predefined_window_start_

Size	predefined_window_start_

Friends
std::ostream &	operator<< (std::ostream &os, ClassicFragmentMover const &cfmover)

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 Attributes inherited from protocols::simple_moves::FragmentMover
core::fragment::FragSetCOP	fragset_

core::kinematics::MoveMapCOP	movemap_

core::fragment::InsertMap	insert_map_

core::fragment::InsertSize	insert_size_

Detailed Description

A FragmentMover that applies uniform sampling of fragments.

Constructor & Destructor Documentation

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP fragset)

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover	(	core::fragment::FragSetCOP	fragset,
		core::kinematics::MoveMapCOP	movemap
	)

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover	(	core::fragment::ConstantLengthFragSet const &	fragset,
		core::kinematics::MoveMap const &	movemap
	)

Temp work around for PyRosetta code, until we found a way how to handle owning pointers in this case

Note: : temp work around for PyRosetta code, until we find a way to handle owning pointers in this case

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::~ClassicFragmentMover ( )

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover	(	core::fragment::FragSetCOP	fragset,
		core::kinematics::MoveMapCOP	movemap,
		std::string	type
	)

protected

alternative Constructor to be used by derived classes

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover	(	core::fragment::FragSetCOP	fragset,
		std::string	type
	)

protected

alternative Constructor to be used by derived classes

References set_defaults().

Member Function Documentation

void protocols::simple_moves::ClassicFragmentMover::apply ( core::pose::Pose & pose)

virtual

Applies classic fragment insertion based on a FragSet.

choose and insert a Fragment from the protocols::moves::Movers Fragment-Set into a Pose.

example: mover_3mer.apply(pose) See also: ClassicFragmentMover Pose ConstantLengthFragSet

Implements protocols::simple_moves::FragmentMover.

References apply_frames(), choose_window_length(), choose_window_start(), protocols::simple_moves::FragmentMover::fragset_, protocols::simple_moves::FragmentMover::insert_size_, min_frag_length_, min_overlap_, protocols::simple_moves::FragmentMover::movemap(), predefined_window_start_, protocols::simple_moves::tr(), protocols::simple_moves::FragmentMover::update_insert_map(), and use_predefined_window_start_.

bool protocols::simple_moves::ClassicFragmentMover::apply_fragment	(	core::fragment::Frame const &	frame,
		Size	frag_num,
		core::kinematics::MoveMap const &	movemap,
		core::pose::Pose &	pose
	)		const

virtual

apply the chosen fragment, this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

Reimplemented in protocols::simple_moves::LoggedFragmentMover, protocols::simple_moves::WobbleMover, and protocols::simple_moves::SymmetricFragmentMover.

Referenced by protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), and apply_frames().

bool protocols::simple_moves::ClassicFragmentMover::apply_frames	(	core::pose::Pose &	,
		core::fragment::FrameList const &
	)		const

protectedvirtual

Implements protocols::simple_moves::FragmentMover.

References apply_fragment(), check_ss(), choose_fragment(), protocols::simple_moves::FragmentMover::movemap_, core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), protocols::simple_moves::tr(), and valid_ss().

Referenced by protocols::simple_moves::FragmentMover::apply(), and apply().

bool protocols::simple_moves::ClassicFragmentMover::check_ss ( ) const

inline

accessor

References check_ss_.

Referenced by apply_frames().

bool protocols::simple_moves::ClassicFragmentMover::choose_fragment	(	core::fragment::FrameList const &	,
		core::pose::Pose const &	,
		Size &	frame_num,
		Size &	frag_num
	)		const

virtual

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found

Reimplemented in protocols::simple_moves::SmoothSymmetricFragmentMover, and protocols::simple_moves::SmoothFragmentMover.

References protocols::forge::build::SegmentInsertConnectionScheme::N, and protocols::simple_moves::RG().

Referenced by apply_frames().

virtual bool protocols::simple_moves::ClassicFragmentMover::choose_window_length	(	core::pose::Pose const &	,
		Size &	window_length
	)		const

inlinevirtual

yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found )

Referenced by apply().

bool protocols::simple_moves::ClassicFragmentMover::choose_window_start	(	core::pose::Pose const &	pose,
		Size	window_length,
		Size &	window_start
	)		const

virtual

yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found )

References bApplyEndBias_, end_bias_check(), protocols::simple_moves::FragmentMover::insert_map_, protocols::simple_moves::FragmentMover::insert_size_, protocols::simple_moves::RG(), and protocols::simple_moves::tr().

Referenced by apply().

void protocols::simple_moves::ClassicFragmentMover::define_start_window ( Size window_start)

apply fragment at predefined position

References predefined_window_start_, and use_predefined_window_start_.

void protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check ( bool setting = true)

inline

References bApplyEndBias_.

core::Real protocols::simple_moves::ClassicFragmentMover::end_bias ( ) const

inline

References end_bias_.

Referenced by end_bias_check().

bool protocols::simple_moves::ClassicFragmentMover::end_bias_check	(	core::pose::Pose const &	pose,
		Size	begin
	)		const

virtual

accept with probability 1 if the fragment window is centered on the center of the protein. accept with probability .3677 if the fragment window is centered end-bias residues away from the center of the protein

References core::kinematics::FoldTree::count_fixed_residues(), end_bias(), core::pose::Pose::fold_tree(), protocols::simple_moves::FragmentMover::insert_size_, core::pose::symmetry::is_symmetric(), protocols::simple_moves::RG(), core::io::serialization::size(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and protocols::simple_moves::tr().

Referenced by choose_window_start().

bool protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled ( ) const

inline

References bApplyEndBias_.

std::string protocols::simple_moves::ClassicFragmentMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::FragmentMover.

Reimplemented in protocols::simple_moves::LoggedFragmentMover, protocols::simple_moves::SmoothSymmetricFragmentMover, protocols::simple_moves::SmoothFragmentMover, protocols::simple_moves::WobbleMover, and protocols::simple_moves::SymmetricFragmentMover.

void protocols::simple_moves::ClassicFragmentMover::on_new_fragments ( )

inlinevirtual

is called from set_fragments()

Reimplemented from protocols::simple_moves::FragmentMover.

void protocols::simple_moves::ClassicFragmentMover::set_check_ss ( bool setting)

inline

check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)

References check_ss_.

void protocols::simple_moves::ClassicFragmentMover::set_defaults ( )

virtual

set defaults

Reimplemented in protocols::simple_moves::WobbleMover.

References bApplyEndBias_, check_ss_, end_bias_, min_frag_length_, min_overlap_, and use_predefined_window_start_.

Referenced by ClassicFragmentMover().

void protocols::simple_moves::ClassicFragmentMover::set_end_bias ( core::Real setting)

inline

References end_bias_.

void protocols::simple_moves::ClassicFragmentMover::set_min_frag_length ( Size setting)

inline

min_frag_length controls the behaviour fragset->region()

References min_frag_length_.

void protocols::simple_moves::ClassicFragmentMover::set_min_overlap ( Size setting)

inline

min_overlap controls the behaviour fragset->region()

References min_overlap_.

bool protocols::simple_moves::ClassicFragmentMover::valid_ss ( std::string const & new_ss) const

virtual

returns true if the ss string is acceptable

DONT ALLOW HELICES OF LESS THAN 3 OR STRANDS OF LESS THAN 2 Fix this: inserting length two helices at the chain end is allowed as is inserting length 1 strands... For the moment, preserving r++'s incorrect behavior.

References protocols::simple_moves::tr().

Referenced by apply_frames().