#include <EnumerateAssemblyMover.hh>

Inheritance diagram for protocols::sewing::EnumerateAssemblyMover:

Public Member Functions
	EnumerateAssemblyMover ()

protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

virtual AssemblyOP	generate_assembly ()

void	parse_my_tag (TagCOP const tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Public Member Functions inherited from protocols::sewing::AssemblyMover
	AssemblyMover ()

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

virtual void	add_starting_model (AssemblyOP assembly) const

virtual core::pose::Pose	get_fullatom_pose (AssemblyOP assembly) const

virtual core::pose::Pose	get_centroid_pose (AssemblyOP assembly) const

bool	follow_random_edge_from_node (AssemblyOP assembly, ModelNode const *reference_node) const

virtual core::pose::Pose	refine_assembly (AssemblyOP &assembly)

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...

void	append_movie_frame (AssemblyOP assembly, core::Size cycle) const

virtual void	output_stats (AssemblyOP const &assembly, core::pose::Pose &pose, std::string indicator_whether_from_MonteCarloAssemblyMover_or_ExhaustiveAssemblyMover)
	add several outputs to the score file Pose can't be const due to scoring. More...

virtual void	parse_requirements (TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)

virtual void	parse_global_requirements (TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)

virtual void	parse_intra_segment_requirements (TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	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

void	set_type (std::string const &setting)

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...

virtual 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)

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...

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...

Private Types
typedef AssemblyMover	parent

Private Attributes
core::Size	bogus_var_for_constructor_

core::Real	min_assembly_score_

std::map< int, Model >	models

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...

Protected Attributes inherited from protocols::sewing::AssemblyMover
scoring::AssemblyScoreFunctionOP	assembly_scorefxn_

SewGraphOP	graph_

std::string	edge_file_

sampling::requirements::RequirementSetOP	requirement_set_

sampling::requirements::RequirementFactory *	requirement_factory_

core::scoring::ScoreFunctionOP	cen_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

core::Real	base_native_bonus_

core::Size	neighbor_cutoff_

Member Typedef Documentation

typedef AssemblyMover protocols::sewing::EnumerateAssemblyMover::parent

private

Constructor & Destructor Documentation

protocols::sewing::EnumerateAssemblyMover::EnumerateAssemblyMover ( )

Referenced by clone().

Member Function Documentation

protocols::moves::MoverOP protocols::sewing::EnumerateAssemblyMover::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. 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.

Reimplemented from protocols::moves::Mover.

References EnumerateAssemblyMover().

protocols::moves::MoverOP protocols::sewing::EnumerateAssemblyMover::fresh_instance ( ) const

virtual

Generates a new Mover object freshly created with the default ctor.

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.

AssemblyOP protocols::sewing::EnumerateAssemblyMover::generate_assembly ( )

virtual

Implements protocols::sewing::AssemblyMover.

References protocols::sewing::AssemblyMover::assembly_scorefxn_, core::graph::Node::const_edge_list_begin(), protocols::sewing::AssemblyFactory::create_assembly(), core::pose::Pose::dump_pdb(), protocols::sewing::AssemblyMover::edge_file_, protocols::sewing::AssemblyMover::get_fullatom_pose(), core::graph::Node::get_node_index(), core::graph::Edge::get_other_ind(), protocols::sewing::AssemblyMover::graph_, min_assembly_score_, protocols::sewing::ModelNode::model(), protocols::sewing::Model::model_id_, models, core::graph::Node::num_edges(), protocols::sewing::AssemblyMover::output_stats(), protocols::sewing::read_model_file(), protocols::sewing::AssemblyMover::requirement_set_, protocols::hybridization::score, protocols::sewing::ModelNode::segment_ids(), protocols::sewing::Model::segments_, core::id::to_string(), and protocols::sewing::TR().

std::string protocols::sewing::EnumerateAssemblyMover::get_name ( ) const

virtual

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

Reimplemented from protocols::sewing::AssemblyMover.

void protocols::sewing::EnumerateAssemblyMover::parse_my_tag	(	TagCOP const	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::sewing::AssemblyMover.

References min_assembly_score_, and protocols::sewing::AssemblyMover::parse_my_tag().