#include <NonlocalFrags.hh>

Inheritance diagram for protocols::frag_picker::nonlocal::NonlocalFrags:

Collaboration diagram for protocols::frag_picker::nonlocal::NonlocalFrags:

Public Member Functions
	NonlocalFrags ()
	Constructs a new mover. More...

void	apply (core::pose::Pose &pose)
	Finds interacting non-local fragment pairs. More...

std::string	get_name () const
	Returns the name of this mover. More...

protocols::moves::MoverOP	clone () const
	Creates a copy of this instance. More...

protocols::moves::MoverOP	fresh_instance () const
	Creates a new instance by calling the no-argument constructor. 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 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

Static Public Member Functions
static void	register_options ()
	Registers applicable options. More...

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...

Private Member Functions
void	initialize ()

bool	recover_checkpoint (const std::string tag, core::pose::Pose &pose)

void	write_checkpoint (const std::string tag, const std::string data)

void	read_checkpoint_file ()

Private Attributes
bool	single_chain_

bool	relax_input_

bool	relax_input_with_coordinate_constraints_

Size	relax_frags_repeats_

std::string	checkpointfile_

std::map< std::string, std::string >	checkpoints_map_

utility::vector1< Size >	frag_sizes_

Size	min_seq_sep_

core::Real	ca_dist_squared_

Size	min_contacts_per_res_

core::Real	max_rmsd_after_relax_

core::Real	max_ddg_score_

bool	output_frags_pdbs_

bool	output_idealized_

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

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 37 of file NonlocalFrags.hh.

Constructor & Destructor Documentation

protocols::frag_picker::nonlocal::NonlocalFrags::NonlocalFrags ( )

Constructs a new mover.

Definition at line 104 of file NonlocalFrags.cc.

References initialize().

Referenced by clone(), and fresh_instance().

Member Function Documentation

void protocols::frag_picker::nonlocal::NonlocalFrags::apply ( core::pose::Pose & pose)

virtual

Finds interacting non-local fragment pairs.

Implements protocols::moves::Mover.

Definition at line 255 of file NonlocalFrags.cc.

References core::pose::add_comment(), core::scoring::angle_constraint, protocols::idealize::IdealizeMover::apply(), core::scoring::atom_pair_constraint, ca_dist_squared_, core::scoring::CA_rmsd(), core::conformation::Residue::chain(), protocols::idealize::IdealizeMover::chainbreaks(), core::kinematics::FoldTree::check_fold_tree(), core::scoring::coordinate_constraint, core::pose::create_subpose(), protocols::jd2::current_output_name(), core::scoring::dihedral_constraint, protocols::idealize::IdealizeMover::fast(), frag_sizes_, protocols::relax::generate_relax_from_cmd(), protocols::jd2::get_current_job(), protocols::jd2::JobDistributor::get_instance(), core::scoring::getScoreFunction(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), max_ddg_score_, max_rmsd_after_relax_, min_contacts_per_res_, min_seq_sep_, core::kinematics::FoldTree::new_jump(), output_frags_pdbs_, output_idealized_, core::pose::Pose::pdb_info(), recover_checkpoint(), relax_frags_repeats_, relax_input_, relax_input_with_coordinate_constraints_, core::pose::Pose::replace_residue(), core::scoring::res_type_constraint, core::pose::Pose::residue(), core::kinematics::FoldTree::set_jump_atoms(), single_chain_, core::pose::Pose::total_residue(), write_checkpoint(), and core::conformation::Residue::xyz().

protocols::moves::MoverOP protocols::frag_picker::nonlocal::NonlocalFrags::clone ( ) const

virtual

Creates a copy of this instance.

Reimplemented from protocols::moves::Mover.

Definition at line 595 of file NonlocalFrags.cc.

References NonlocalFrags().

protocols::moves::MoverOP protocols::frag_picker::nonlocal::NonlocalFrags::fresh_instance ( ) const

virtual

Creates a new instance by calling the no-argument constructor.

Reimplemented from protocols::moves::Mover.

Definition at line 599 of file NonlocalFrags.cc.

References NonlocalFrags().

std::string protocols::frag_picker::nonlocal::NonlocalFrags::get_name ( ) const

virtual

Returns the name of this mover.

Implements protocols::moves::Mover.

Definition at line 591 of file NonlocalFrags.cc.

void protocols::frag_picker::nonlocal::NonlocalFrags::initialize ( )

private

Definition at line 121 of file NonlocalFrags.cc.

References ca_dist_squared_, frag_sizes_, max_ddg_score_, max_rmsd_after_relax_, min_contacts_per_res_, min_seq_sep_, output_frags_pdbs_, output_idealized_, read_checkpoint_file(), relax_frags_repeats_, relax_input_, relax_input_with_coordinate_constraints_, and single_chain_.

Referenced by NonlocalFrags().

void protocols::frag_picker::nonlocal::NonlocalFrags::read_checkpoint_file ( )

private

Definition at line 227 of file NonlocalFrags.cc.

References checkpointfile_, checkpoints_map_, and protocols::swa::rna::file_exists().

Referenced by initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::recover_checkpoint	(	const std::string	tag,
		core::pose::Pose &	pose
	)

private

Definition at line 181 of file NonlocalFrags.cc.

References core::pose::add_comment(), checkpoints_map_, and core::io::serialization::size().

Referenced by apply().

void protocols::frag_picker::nonlocal::NonlocalFrags::register_options ( )

static

Registers applicable options.

Definition at line 78 of file NonlocalFrags.cc.

void protocols::frag_picker::nonlocal::NonlocalFrags::write_checkpoint	(	const std::string	tag,
		const std::string	data
	)

private

Definition at line 193 of file NonlocalFrags.cc.

References checkpointfile_, and checkpoints_map_.

Referenced by apply().

Member Data Documentation

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::ca_dist_squared_

private

Definition at line 82 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

std::string protocols::frag_picker::nonlocal::NonlocalFrags::checkpointfile_

private

Definition at line 76 of file NonlocalFrags.hh.

Referenced by read_checkpoint_file(), and write_checkpoint().

std::map< std::string, std::string > protocols::frag_picker::nonlocal::NonlocalFrags::checkpoints_map_

private

Definition at line 77 of file NonlocalFrags.hh.

Referenced by read_checkpoint_file(), recover_checkpoint(), and write_checkpoint().

utility::vector1<Size> protocols::frag_picker::nonlocal::NonlocalFrags::frag_sizes_

private

Definition at line 79 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::max_ddg_score_

private

Definition at line 85 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

core::Real protocols::frag_picker::nonlocal::NonlocalFrags::max_rmsd_after_relax_

private

Definition at line 84 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

Size protocols::frag_picker::nonlocal::NonlocalFrags::min_contacts_per_res_

private

Definition at line 83 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

Size protocols::frag_picker::nonlocal::NonlocalFrags::min_seq_sep_

private

Definition at line 81 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::output_frags_pdbs_

private

Definition at line 87 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::output_idealized_

private

Definition at line 88 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

Size protocols::frag_picker::nonlocal::NonlocalFrags::relax_frags_repeats_

private

Definition at line 74 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::relax_input_

private

Definition at line 72 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::relax_input_with_coordinate_constraints_

private

Definition at line 73 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

bool protocols::frag_picker::nonlocal::NonlocalFrags::single_chain_

private

Definition at line 71 of file NonlocalFrags.hh.

Referenced by apply(), and initialize().

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

src/protocols/frag_picker/nonlocal/NonlocalFrags.hh
src/protocols/frag_picker/nonlocal/NonlocalFrags.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation