Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much. More...

#include <FastGapMover.hh>

Inheritance diagram for protocols::loophash::FastGapMover:

[legend]

Collaboration diagram for protocols::loophash::FastGapMover:

[legend]

Public Types
typedef core::Size	Size

typedef core::Real	Real

typedef core::pose::Pose	Pose

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

Public Member Functions
	FastGapMover ()

virtual moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual moves::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	apply (Pose &pose)

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

FastGapMover &	min_rms (core::Real const setting)

FastGapMover &	max_rms (core::Real const setting)

FastGapMover &	non_ideal (bool const setting)

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	find_next_gap (Pose &pose, Size &idx, Real &gap_distance)

Private Attributes
LocalInserter_SimpleMinOP	simple_inserter_

LoopHashLibraryOP	lhlibrary_

LoopHashSamplerOP	lhsampler_

core::Size	min_loop_size_

core::Size	max_loop_size_

core::Real	max_rms_

core::Real	min_rms_

bool	non_ideal_

Additional Inherited Members
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

Mover class for closing gaps. This Mover checks for any gaps using residue residue distances Then eats back at the chain surrounding it until loophash finds a fragment that fits in the space without changing the rest of pose too much.

Definition at line 38 of file FastGapMover.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::loophash::FastGapMover::Pose

Definition at line 43 of file FastGapMover.hh.

typedef core::Real protocols::loophash::FastGapMover::Real

Definition at line 42 of file FastGapMover.hh.

typedef core::Size protocols::loophash::FastGapMover::Size

Definition at line 41 of file FastGapMover.hh.

Constructor & Destructor Documentation

protocols::loophash::FastGapMover::FastGapMover ( )

Definition at line 82 of file FastGapMover.cc.

References lhlibrary_, lhsampler_, max_loop_size_, min_loop_size_, and simple_inserter_.

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::loophash::FastGapMover::apply ( pose::Pose & pose)

virtual

Implements protocols::moves::Mover.

Definition at line 104 of file FastGapMover.cc.

References core::chemical::CENTROID, find_next_gap(), lhsampler_, max_loop_size_, max_rms_, min_loop_size_, min_rms_, non_ideal_, core::util::switch_to_residue_type_set(), and protocols::loophash::TR().

virtual moves::MoverOP protocols::loophash::FastGapMover::clone ( ) const

inlinevirtual

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

Reimplemented from protocols::moves::Mover.

Definition at line 48 of file FastGapMover.hh.

References FastGapMover().

void protocols::loophash::FastGapMover::find_next_gap	(	Pose &	pose,
		Size &	idx,
		Real &	gap_distance
	)

private

Definition at line 147 of file FastGapMover.cc.

References core::conformation::Residue::atom(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_polymer(), core::conformation::Residue::lower_connect_atom(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::conformation::Residue::upper_connect_atom(), and protocols::kinmatch::xyz().

Referenced by apply().

virtual moves::MoverOP protocols::loophash::FastGapMover::fresh_instance ( ) const

inlinevirtual

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).

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.

Definition at line 52 of file FastGapMover.hh.

References FastGapMover().

string protocols::loophash::FastGapMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 172 of file FastGapMover.cc.

FastGapMover& protocols::loophash::FastGapMover::max_rms ( core::Real const setting)

inline

Definition at line 69 of file FastGapMover.hh.

References max_rms_.

FastGapMover& protocols::loophash::FastGapMover::min_rms ( core::Real const setting)

inline

Definition at line 62 of file FastGapMover.hh.

References min_rms_.

FastGapMover& protocols::loophash::FastGapMover::non_ideal ( bool const setting)

inline

Definition at line 76 of file FastGapMover.hh.

References non_ideal_.

Member Data Documentation

LoopHashLibraryOP protocols::loophash::FastGapMover::lhlibrary_

private

Definition at line 90 of file FastGapMover.hh.

Referenced by FastGapMover().

LoopHashSamplerOP protocols::loophash::FastGapMover::lhsampler_

private

Definition at line 91 of file FastGapMover.hh.

Referenced by apply(), and FastGapMover().

core::Size protocols::loophash::FastGapMover::max_loop_size_

private

Definition at line 94 of file FastGapMover.hh.

Referenced by apply(), and FastGapMover().

core::Real protocols::loophash::FastGapMover::max_rms_

private

Definition at line 95 of file FastGapMover.hh.

Referenced by apply(), and max_rms().

core::Size protocols::loophash::FastGapMover::min_loop_size_

private

Definition at line 93 of file FastGapMover.hh.

Referenced by apply(), and FastGapMover().

core::Real protocols::loophash::FastGapMover::min_rms_

private

Definition at line 96 of file FastGapMover.hh.

Referenced by apply(), and min_rms().

bool protocols::loophash::FastGapMover::non_ideal_

private

Definition at line 97 of file FastGapMover.hh.

Referenced by apply(), and non_ideal().

LocalInserter_SimpleMinOP protocols::loophash::FastGapMover::simple_inserter_

private

Definition at line 89 of file FastGapMover.hh.

Referenced by FastGapMover().

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

src/protocols/loophash/FastGapMover.hh
src/protocols/loophash/FastGapMover.cc

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation