#include <cluster.hh>

Inheritance diagram for protocols::cluster::ClusterPhilStyle_Loop:

Collaboration diagram for protocols::cluster::ClusterPhilStyle_Loop:

Public Member Functions
	ClusterPhilStyle_Loop (protocols::loops::Loops loop_def)

virtual	~ClusterPhilStyle_Loop ()

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

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

virtual core::Real	get_distance_measure (const core::pose::Pose &pose1, const core::pose::Pose &pose2) const

Public Member Functions inherited from protocols::cluster::ClusterPhilStyle
	ClusterPhilStyle ()

virtual	~ClusterPhilStyle ()

virtual void	do_clustering (core::Size max_total_cluster)

void	do_redistribution ()

Public Member Functions inherited from protocols::cluster::ClusterBase
	ClusterBase ()

void	set_cluster_radius (core::Real cluster_radius)

void	set_population_weight (core::Real population_weight)

core::Real	get_cluster_radius ()

core::Real	get_median_rms ()

void	calculate_distance_matrix ()

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

void	remove_highest_energy_member_of_each_group ()

void	sort_each_group_by_energy ()

void	sort_groups_by_energy ()

void	remove_singletons ()

void	export_only_low (bool value=false)

void	limit_groupsize (int limit=-1)

void	limit_groupsize (core::Real percent_limit)

void	random_limit_groupsize (core::Real percent_limit)

void	limit_groups (int limit=-1)

void	limit_total_structures (int limit=-1)

void	clean_pose_store ()

void	print_summary ()

void	print_raw_numbers ()

void	print_cluster_assignment ()

void	print_cluster_PDBs (std::string prefix)

void	print_clusters_silentfile (std::string prefix)

std::vector< core::pose::PoseOP >	return_lowest_poses_in_clusters ()

std::vector< core::pose::PoseOP >	return_top_poses_in_clusters (core::Size count)

void	create_constraints (std::string prefix, EnsembleConstraints &constraint_maker)

std::vector< Cluster > const &	get_cluster_list () const

Public Member Functions inherited from protocols::cluster::GatherPosesMover
	GatherPosesMover ()

void	set_score_function (core::scoring::ScoreFunctionOP sfxn)

void	set_filter (core::Real filter)

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

bool	check_tag (const std::string &query_tag)

void	push_back (const core::pose::Pose &pose)

void	clear ()

void	set_cluster_by_protein_backbone (bool const &setting)

void	set_cluster_by_all_atom (bool const &setting)

int	processed () const

std::vector< core::pose::Pose > &	get_pose_list ()

std::vector< std::string > const &	get_tag_list () 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 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

Private Attributes
protocols::loops::Loops	loop_def_

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 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::cluster::ClusterBase
ObjexxFCL::FArray2D< core::Real >	distance_matrix

std::vector< Cluster >	clusterlist

bool	export_only_low_

core::Real	median_rms_

core::Real	population_weight_

core::Real	cluster_radius_

Detailed Description

Definition at line 265 of file cluster.hh.

Constructor & Destructor Documentation

protocols::cluster::ClusterPhilStyle_Loop::ClusterPhilStyle_Loop ( protocols::loops::Loops loop_def)

inline

Definition at line 267 of file cluster.hh.

Referenced by clone().

virtual protocols::cluster::ClusterPhilStyle_Loop::~ClusterPhilStyle_Loop ( )

inlinevirtual

Definition at line 271 of file cluster.hh.

Member Function Documentation

protocols::moves::MoverOP protocols::cluster::ClusterPhilStyle_Loop::clone ( ) const

inlinevirtual

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

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::cluster::ClusterPhilStyle.

Definition at line 273 of file cluster.hh.

References ClusterPhilStyle_Loop().