protocols::cluster Namespace Reference

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

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 thread_local 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Function Documentation

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().

template<typename T >

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

inline

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

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

(

const std::string

filename

)

References getline(), and utility_exit_with_message.

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

static thread_local 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

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