protocols::cluster Namespace Reference

Classes
class	Exemplar
	Data structure for one similarity measurement (s_ik) for affinity propagation clustering. More...
class	DataPoint
	Data structure for one input data point for affinity propagation clustering. More...
class	APCluster
	Public interface for doing affinity propagation clustering. More...
class	GatherPosesMover
class	EnsembleConstraints
class	EnsembleConstraints_Simple
struct	Cluster
class	ClusterBase
class	ClusterPhilStyle
class	ClusterPhilStyle_Loop
class	AssignToClustersMover

Typedefs
typedef utility::pointer::owning_ptr < APCluster >	APClusterOP
typedef utility::pointer::owning_ptr < APCluster const >	APClusterCOP
typedef utility::pointer::owning_ptr < GatherPosesMover >	GatherPosesMoverOP
typedef utility::pointer::owning_ptr < GatherPosesMover const >	GatherPosesMoverCOP
typedef utility::pointer::owning_ptr < EnsembleConstraints >	EnsembleConstraintsOP
typedef utility::pointer::owning_ptr < EnsembleConstraints const >	EnsembleConstraintsCOP
typedef utility::pointer::owning_ptr < EnsembleConstraints_Simple >	EnsembleConstraints_SimpleOP
typedef utility::pointer::owning_ptr < EnsembleConstraints_Simple const >	EnsembleConstraints_SimpleCOP
typedef utility::pointer::owning_ptr < ClusterBase >	ClusterBaseOP
typedef utility::pointer::owning_ptr < ClusterBase const >	ClusterBaseCOP
typedef utility::pointer::owning_ptr < ClusterPhilStyle >	ClusterPhilStyleOP
typedef utility::pointer::owning_ptr < ClusterPhilStyle const >	ClusterPhilStyleCOP
typedef utility::pointer::owning_ptr < AssignToClustersMover >	AssignToClustersMoverOP
typedef utility::pointer::owning_ptr < AssignToClustersMover const >	AssignToClustersMoverCOP

Functions
template<typename T >
void	write1 (FILE *f, T t)
template<typename T >
void	read1 (FILE *f, T &t)
static basic::Tracer	tr ("protocols.cluster")
static numeric::random::RandomGenerator	RG (42032)
std::map< std::string, core::Real >	read_template_scores (const std::string filename)
bool	compareIndexEnergyPair (const std::pair< int, Real > &p1, const std::pair< int, Real > &p2)

Typedef Documentation

typedef utility::pointer::owning_ptr< APCluster const > protocols::cluster::APClusterCOP

Definition at line 27 of file APCluster.fwd.hh.

typedef utility::pointer::owning_ptr< APCluster > protocols::cluster::APClusterOP

Definition at line 25 of file APCluster.fwd.hh.

typedef utility::pointer::owning_ptr< AssignToClustersMover const > protocols::cluster::AssignToClustersMoverCOP

Definition at line 289 of file cluster.hh.

typedef utility::pointer::owning_ptr< AssignToClustersMover > protocols::cluster::AssignToClustersMoverOP

Definition at line 287 of file cluster.hh.

typedef utility::pointer::owning_ptr< ClusterBase const > protocols::cluster::ClusterBaseCOP

Definition at line 136 of file cluster.hh.

typedef utility::pointer::owning_ptr< ClusterBase > protocols::cluster::ClusterBaseOP

Definition at line 134 of file cluster.hh.

typedef utility::pointer::owning_ptr< ClusterPhilStyle const > protocols::cluster::ClusterPhilStyleCOP

Definition at line 251 of file cluster.hh.

typedef utility::pointer::owning_ptr< ClusterPhilStyle > protocols::cluster::ClusterPhilStyleOP

Definition at line 249 of file cluster.hh.

typedef utility::pointer::owning_ptr< EnsembleConstraints_Simple const > protocols::cluster::EnsembleConstraints_SimpleCOP

Definition at line 114 of file cluster.hh.

typedef utility::pointer::owning_ptr< EnsembleConstraints_Simple > protocols::cluster::EnsembleConstraints_SimpleOP

Definition at line 112 of file cluster.hh.

typedef utility::pointer::owning_ptr< EnsembleConstraints const > protocols::cluster::EnsembleConstraintsCOP

Definition at line 97 of file cluster.hh.

typedef utility::pointer::owning_ptr< EnsembleConstraints > protocols::cluster::EnsembleConstraintsOP

Definition at line 95 of file cluster.hh.

typedef utility::pointer::owning_ptr< GatherPosesMover const > protocols::cluster::GatherPosesMoverCOP

Definition at line 38 of file cluster.hh.

typedef utility::pointer::owning_ptr< GatherPosesMover > protocols::cluster::GatherPosesMoverOP

Definition at line 36 of file cluster.hh.

Function Documentation

bool protocols::cluster::compareIndexEnergyPair	(	const std::pair< int, Real > &	p1,
		const std::pair< int, Real > &	p2
	)

Definition at line 102 of file cluster.cc.

Referenced by protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), and protocols::cluster::ClusterBase::sort_groups_by_energy().

template<typename T >

void protocols::cluster::read1 ( FILE *  f, T &  t  )

inline

Definition at line 440 of file APCluster.cc.

References core::pack::interaction_graph::T().

Referenced by protocols::cluster::APCluster::load_binary().

std::map< std::string, core::Real > protocols::cluster::read_template_scores

(

const std::string

filename)

Definition at line 77 of file cluster.cc.

Referenced by protocols::cluster::GatherPosesMover::GatherPosesMover().

static numeric::random::RandomGenerator protocols::cluster::RG ( 42032  )

static

Referenced by protocols::cluster::Cluster::shuffle().

static basic::Tracer protocols::cluster::tr ( "protocols.cluster"  )

static

Referenced by protocols::cluster::ClusterBase::add_structure(), protocols::cluster::GatherPosesMover::apply(), protocols::cluster::AssignToClustersMover::apply(), protocols::cluster::ClusterBase::calculate_distance_matrix(), protocols::cluster::ClusterBase::clean_pose_store(), protocols::cluster::ClusterBase::create_constraints(), protocols::cluster::ClusterPhilStyle::do_clustering(), protocols::cluster::ClusterPhilStyle::do_redistribution(), protocols::cluster::GatherPosesMover::GatherPosesMover(), protocols::cluster::GatherPosesMover::get_distance_measure(), protocols::cluster::ClusterBase::limit_groups(), protocols::cluster::ClusterBase::limit_groupsize(), protocols::cluster::ClusterBase::limit_total_structures(), protocols::cluster::ClusterBase::print_cluster_assignment(), protocols::cluster::ClusterBase::print_raw_numbers(), protocols::cluster::ClusterBase::print_summary(), protocols::cluster::ClusterBase::random_limit_groupsize(), protocols::cluster::ClusterBase::remove_highest_energy_member_of_each_group(), protocols::cluster::ClusterBase::sort_each_group_by_energy(), and protocols::cluster::ClusterBase::sort_groups_by_energy().

template<typename T >

void protocols::cluster::write1 ( FILE *  f, T  t  )

inline

Definition at line 438 of file APCluster.cc.

References core::pack::interaction_graph::T().

Referenced by protocols::cluster::APCluster::save_binary().