protocols::cluster Namespace Reference

Namespaces
	calibur

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	ClusterPhilStyle_PoseReporter
class	AssignToClustersMover

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

APClusterCOP

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

APClusterOP

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

AssignToClustersMoverCOP

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

AssignToClustersMoverOP

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

ClusterBaseCOP

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

ClusterBaseOP

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

ClusterPhilStyleCOP

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

ClusterPhilStyleOP

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

EnsembleConstraints_SimpleCOP

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

EnsembleConstraints_SimpleOP

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

EnsembleConstraintsCOP

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

EnsembleConstraintsOP

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

GatherPosesMoverCOP

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

GatherPosesMoverOP

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

Function Documentation

compareIndexEnergyPair()

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

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().

read1()

template<typename T >

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

inline

References protocols::hybridization::t.

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

read_template_scores()

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

(

const std::string &

filename

)

References protocols::abinitio::filename().

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

tr()

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().

write1()

template<typename T >

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

inline

References protocols::hybridization::t.

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