protocols::toolbox::ClusterBase Class Reference

#include <Cluster.hh>

Inheritance diagram for protocols::toolbox::ClusterBase:

Public Types
typedef std::deque< core::Size >	Cluster
typedef utility::vector1< Cluster >	ClusterList
typedef Cluster::const_iterator	IntraClusterIterator
typedef ClusterList::const_iterator	ClusterIterator

Public Member Functions
	ClusterBase (core::Size dim)
core::Real	dist (core::Size i, core::Size j) const
core::Real &	dist (core::Size i, core::Size j)
ObjexxFCL::FArray2D< core::Real > &	distance_matrix ()
ObjexxFCL::FArray2D< core::Real > const &	distance_matrix () const
core::Size	dim () const
void	print_cluster_assignment (std::ostream &out) const
core::Size	size () const
Cluster const &	cluster (core::Size i) const
ClusterList const &	clusterlist () const
void	sort_each_group_by_energy (utility::vector1< core::Real > all_energies, bool keep_center=false)
void	limit_groupsize (core::Size limit)
void	print_summary (utility::vector1< std::string > tags, utility::vector1< core::Real > all_energies)
void	show (std::ostream &out) const
void	read (std::istream &in)

Protected Attributes
ClusterList	clusterlist_
ObjexxFCL::FArray2D< core::Real >	distance_
core::Size	dim_

Member Typedef Documentation

Cluster

typedef std::deque< core::Size > protocols::toolbox::ClusterBase::Cluster

ClusterIterator

typedef ClusterList::const_iterator protocols::toolbox::ClusterBase::ClusterIterator

ClusterList

typedef utility::vector1< Cluster > protocols::toolbox::ClusterBase::ClusterList

IntraClusterIterator

typedef Cluster::const_iterator protocols::toolbox::ClusterBase::IntraClusterIterator

Constructor & Destructor Documentation

ClusterBase()

protocols::toolbox::ClusterBase::ClusterBase ( core::Size  dim )

inline

Member Function Documentation

cluster()

Cluster const& protocols::toolbox::ClusterBase::cluster ( core::Size  i ) const

inline

References clusterlist_.

clusterlist()

ClusterList const& protocols::toolbox::ClusterBase::clusterlist ( ) const

inline

References clusterlist_.

Referenced by protocols::toolbox::cluster_silent_structs().

dim()

core::Size protocols::toolbox::ClusterBase::dim ( ) const

inline

References dim_.

Referenced by protocols::toolbox::ClusterPhilStyle::compute().

dist() [1/2]

core::Real& protocols::toolbox::ClusterBase::dist ( core::Size  i, core::Size  j  )

inline

References distance_.

dist() [2/2]

core::Real protocols::toolbox::ClusterBase::dist ( core::Size  i, core::Size  j  ) const

inline

References distance_.

Referenced by protocols::toolbox::ClusterPhilStyle::compute(), and print_summary().

distance_matrix() [1/2]

ObjexxFCL::FArray2D< core::Real >& protocols::toolbox::ClusterBase::distance_matrix ( )

inline

References distance_.

Referenced by protocols::toolbox::cluster_silent_structs().

distance_matrix() [2/2]

ObjexxFCL::FArray2D< core::Real > const& protocols::toolbox::ClusterBase::distance_matrix ( ) const

inline

References distance_.

limit_groupsize()

void protocols::toolbox::ClusterBase::limit_groupsize

(

core::Size

limit

)

References clusterlist_.

Referenced by protocols::toolbox::cluster_silent_structs().

print_cluster_assignment()

void protocols::toolbox::ClusterBase::print_cluster_assignment

(

std::ostream &

out

)

const

References clusterlist_, and core::conformation::membrane::out.

print_summary()

void protocols::toolbox::ClusterBase::print_summary	(	utility::vector1< std::string >	tags,
		utility::vector1< core::Real >	all_energies
	)

References clusterlist_, dist(), and protocols::toolbox::tr().

Referenced by protocols::toolbox::cluster_silent_structs().

read()

void protocols::toolbox::ClusterBase::read

(

std::istream &

in

)

References clusterlist_, and core::conformation::membrane::in.

Referenced by protocols::toolbox::operator>>().

show()

void protocols::toolbox::ClusterBase::show

(

std::ostream &

out

)

const

References clusterlist_, and core::conformation::membrane::out.

Referenced by protocols::toolbox::operator<<().

size()

core::Size protocols::toolbox::ClusterBase::size ( ) const

inline

References clusterlist_.

sort_each_group_by_energy()

void protocols::toolbox::ClusterBase::sort_each_group_by_energy	(	utility::vector1< core::Real >	all_energies,
		bool	keep_center = false
	)

References clusterlist_, protocols::toolbox::compareIndexEnergyPair(), and protocols::hybridization::score.

Referenced by protocols::toolbox::cluster_silent_structs().

Member Data Documentation

clusterlist_

ClusterList protocols::toolbox::ClusterBase::clusterlist_

protected

Referenced by cluster(), clusterlist(), protocols::toolbox::ClusterPhilStyle::compute(), limit_groupsize(), print_cluster_assignment(), print_summary(), read(), show(), size(), and sort_each_group_by_energy().

dim_

core::Size protocols::toolbox::ClusterBase::dim_

protected

Referenced by dim().

distance_

ObjexxFCL::FArray2D< core::Real > protocols::toolbox::ClusterBase::distance_

protected

Referenced by dist(), and distance_matrix().

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The documentation for this class was generated from the following files:

• src/protocols/toolbox/Cluster.hh
• src/protocols/toolbox/Cluster.cc