protocols::toolbox::CalcInterNeighborGroup Class Reference

#include <CalcInterNeighborGroup.hh>

Inheritance diagram for protocols::toolbox::CalcInterNeighborGroup:

Public Types
typedef std::set< core::Size >	one_group
typedef std::pair< one_group, one_group >	group_pair
typedef utility::vector1< group_pair >	group_set

Public Member Functions
	CalcInterNeighborGroup ()
	CalcInterNeighborGroup (group_set const &groups, core::Real dist_cutoff=10.0)
	CalcInterNeighborGroup (CalcInterNeighborGroup const &calculator)
	~CalcInterNeighborGroup () override
void	compute (core::pose::Pose const &pose)
void	dist_cutoff (core::Real cutoff)
core::Real	dist_cutoff () const
	return distance cutoff More...
group_set const &	groups () const
void	groups (group_set groups)
core::Real	num_neighbors ()
std::set< core::Size >	neighbors ()

Private Attributes
group_set	groups_
	stores the input - whose neighbors are we finding? More...
core::Real	dist_cutoff_
	stores the input - how far away is a neighbor? More...
core::Size	num_neighbors_
	the number of neighbors in the set neighbors_ More...
std::set< core::Size >	neighbors_
	the set of neighbors to return - union of interfaces between groups More...

Detailed Description

This is complicated, so pay attention. You define groups of residues within a protein (say, the N and C terminal domains). You then define which pairs of groups you are interested in. This calculator returns the union of the sets of residues at the interfaces between these domains/groups. Functionally it is intended for "interface design" at the non-chainbreak interface between domains of multidomain proteins. It contains a superset of the functionality of some of the other calculators (so I'll be obsoleting them, maybe?). The pose does NOT have to have been scored.

• "groups" string returns the input groups; of type utility::vector1< std::pair< std::set< core::Size >, std::set< core::Size > > > (not a calculated value)
• "dist_cutoff" returns the input cutoff distance for neighbor finding (not a calculated value)
• "neighbors" returns a std::set<core::Size> of the neighbors calculated between the group pairs.
• "num_neighbors" returns the size of the neighbors set.

Member Typedef Documentation

group_pair

typedef std::pair< one_group, one_group > protocols::toolbox::CalcInterNeighborGroup::group_pair

group_set

typedef utility::vector1< group_pair > protocols::toolbox::CalcInterNeighborGroup::group_set

one_group

typedef std::set< core::Size > protocols::toolbox::CalcInterNeighborGroup::one_group

Constructor & Destructor Documentation

CalcInterNeighborGroup() [1/3]

protocols::toolbox::CalcInterNeighborGroup::CalcInterNeighborGroup

(

)

References dist_cutoff_, and num_neighbors_.

CalcInterNeighborGroup() [2/3]

protocols::toolbox::CalcInterNeighborGroup::CalcInterNeighborGroup	(	group_set const &	groups,
		core::Real	dist_cutoff = 10.0
	)

CalcInterNeighborGroup() [3/3]

protocols::toolbox::CalcInterNeighborGroup::CalcInterNeighborGroup

(

CalcInterNeighborGroup const &

calculator

)

~CalcInterNeighborGroup()

protocols::toolbox::CalcInterNeighborGroup::~CalcInterNeighborGroup ( )

overridedefault

Member Function Documentation

compute()

void protocols::toolbox::CalcInterNeighborGroup::compute

(

core::pose::Pose const &

pose

)

References core::pose::Pose::conformation(), dist_cutoff_, core::sequence::end, groups_, neighbors_, num_neighbors_, core::conformation::residue_point_graph_from_conformation(), and core::pose::Pose::size().

Referenced by protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), and protocols::interface::select_interface_residues().

dist_cutoff() [1/2]

core::Real protocols::toolbox::CalcInterNeighborGroup::dist_cutoff ( ) const

inline

return distance cutoff

References dist_cutoff_.

dist_cutoff() [2/2]

void protocols::toolbox::CalcInterNeighborGroup::dist_cutoff ( core::Real  cutoff )

inline

References dist_cutoff_.

groups() [1/2]

group_set const& protocols::toolbox::CalcInterNeighborGroup::groups ( ) const

inline

References groups_.

groups() [2/2]

void protocols::toolbox::CalcInterNeighborGroup::groups ( group_set  groups )

inline

References groups(), and groups_.

Referenced by groups().

neighbors()

std::set< core::Size > protocols::toolbox::CalcInterNeighborGroup::neighbors ( )

inline

References neighbors_.

Referenced by protocols::analysis::InterfaceAnalyzerMover::make_multichain_interface_set(), and protocols::interface::select_interface_residues().

num_neighbors()

core::Real protocols::toolbox::CalcInterNeighborGroup::num_neighbors ( )

inline

References num_neighbors_.

Member Data Documentation

dist_cutoff_

core::Real protocols::toolbox::CalcInterNeighborGroup::dist_cutoff_

private

stores the input - how far away is a neighbor?

Referenced by CalcInterNeighborGroup(), compute(), and dist_cutoff().

groups_

group_set protocols::toolbox::CalcInterNeighborGroup::groups_

private

stores the input - whose neighbors are we finding?

Referenced by compute(), and groups().

neighbors_

std::set< core::Size > protocols::toolbox::CalcInterNeighborGroup::neighbors_

private

the set of neighbors to return - union of interfaces between groups

Referenced by compute(), and neighbors().

num_neighbors_

core::Size protocols::toolbox::CalcInterNeighborGroup::num_neighbors_

private

the number of neighbors in the set neighbors_

Referenced by CalcInterNeighborGroup(), compute(), and num_neighbors().

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

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