Public Types | Public Member Functions | Private Attributes | List of all members
protocols::toolbox::CalcInterNeighborGroup Class Reference

#include <CalcInterNeighborGroup.hh>

Inheritance diagram for protocols::toolbox::CalcInterNeighborGroup:
Inheritance graph

Public Types

typedef std::set< core::Sizeone_group
typedef std::pair< one_group, one_groupgroup_pair
typedef utility::vector1< group_pairgroup_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::Sizeneighbors ()

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::Sizeneighbors_
 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.

Member Typedef Documentation

◆ group_pair

◆ group_set

◆ 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 ( )

Member Function Documentation

◆ compute()

void protocols::toolbox::CalcInterNeighborGroup::compute ( core::pose::Pose const &  pose)

◆ dist_cutoff() [1/2]

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

return distance cutoff

References dist_cutoff_.

◆ dist_cutoff() [2/2]

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

References dist_cutoff_.

◆ groups() [1/2]

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

References groups_.

◆ groups() [2/2]

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

References groups(), and groups_.

Referenced by groups().

◆ neighbors()

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

◆ num_neighbors()

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

References num_neighbors_.

Member Data Documentation

◆ dist_cutoff_

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

stores the input - how far away is a neighbor?

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

◆ groups_

group_set protocols::toolbox::CalcInterNeighborGroup::groups_

stores the input - whose neighbors are we finding?

Referenced by compute(), and groups().

◆ neighbors_

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

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_

the number of neighbors in the set neighbors_

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

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