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protocols::pose_metric_calculators::InterGroupNeighborsCalculator Class Reference

#include <InterGroupNeighborsCalculator.hh>

Inheritance diagram for protocols::pose_metric_calculators::InterGroupNeighborsCalculator:
Inheritance graph
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Public Types

typedef
core::pose::metrics::StructureDependentCalculator 
parent
 
typedef std::set< core::Sizeone_group
 
typedef std::pair< one_group,
one_group
group_pair
 
typedef utility::vector1
< group_pair
group_set
 

Public Member Functions

 InterGroupNeighborsCalculator (group_set const &groups, core::Real dist_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::inter_group_neighbors_cutoff])
 
core::pose::metrics::PoseMetricCalculatorOP clone () const override
 
group_set const & groups () const
 return groups More...
 
core::Real dist_cutoff () const
 return distance cutoff More...
 
- Public Member Functions inherited from core::pose::metrics::StructureDependentCalculator
 StructureDependentCalculator ()
 
void notify_structure_change () override
 
void get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose) override
 
std::string get (std::string const &key, Pose const &this_pose) override
 
- Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
 PoseMetricCalculator ()
 
virtual void notify_energy_change ()
 

Protected Member Functions

void lookup (std::string const &key, basic::MetricValueBase *valptr) const override
 
std::string print (std::string const &key) const override
 
void recompute (core::pose::Pose const &pose) override
 

Private Attributes

toolbox::CalcInterNeighborGroupOP calc_inter_group_
 
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

Constructor & Destructor Documentation

protocols::pose_metric_calculators::InterGroupNeighborsCalculator::InterGroupNeighborsCalculator ( group_set const &  groups,
core::Real  dist_cutoff = basic::options::option[basic::options::OptionKeys::pose_metrics::inter_group_neighbors_cutoff] 
)

Member Function Documentation

core::pose::metrics::PoseMetricCalculatorOP protocols::pose_metric_calculators::InterGroupNeighborsCalculator::clone ( ) const
overridevirtual
core::Real protocols::pose_metric_calculators::InterGroupNeighborsCalculator::dist_cutoff ( ) const

return distance cutoff

References dist_cutoff_.

Referenced by InterGroupNeighborsCalculator().

group_set const & protocols::pose_metric_calculators::InterGroupNeighborsCalculator::groups ( ) const

return groups

References groups_.

Referenced by InterGroupNeighborsCalculator().

void protocols::pose_metric_calculators::InterGroupNeighborsCalculator::lookup ( std::string const &  key,
basic::MetricValueBase *  valptr 
) const
overrideprotectedvirtual
std::string protocols::pose_metric_calculators::InterGroupNeighborsCalculator::print ( std::string const &  key) const
overrideprotectedvirtual
void protocols::pose_metric_calculators::InterGroupNeighborsCalculator::recompute ( core::pose::Pose const &  pose)
overrideprotectedvirtual

Member Data Documentation

toolbox::CalcInterNeighborGroupOP protocols::pose_metric_calculators::InterGroupNeighborsCalculator::calc_inter_group_
private
core::Real protocols::pose_metric_calculators::InterGroupNeighborsCalculator::dist_cutoff_
private

stores the input - how far away is a neighbor?

Referenced by dist_cutoff(), lookup(), print(), and recompute().

group_set protocols::pose_metric_calculators::InterGroupNeighborsCalculator::groups_
private

stores the input - whose neighbors are we finding?

Referenced by groups(), lookup(), print(), and recompute().

std::set< core::Size > protocols::pose_metric_calculators::InterGroupNeighborsCalculator::neighbors_
private

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

Referenced by lookup(), print(), and recompute().

core::Size protocols::pose_metric_calculators::InterGroupNeighborsCalculator::num_neighbors_
private

the number of neighbors in the set neighbors_

Referenced by lookup(), print(), and recompute().


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