protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator Class Reference

#include <InterGroupNeighborsCalculator.hh>

Inheritance diagram for protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator:

Public Types
typedef core::pose::metrics::StructureDependentCalculator	parent
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
	InterGroupNeighborsCalculator (group_set const &groups, core::Real dist_cutoff=basic::options::option[basic::options::OptionKeys::pose_metrics::inter_group_neighbors_cutoff])
	InterGroupNeighborsCalculator (InterGroupNeighborsCalculator const &calculator)
	~InterGroupNeighborsCalculator ()
virtual core::pose::metrics::PoseMetricCalculatorOP	clone () const
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 ()
void	get (std::string const &key, basic::MetricValueBase &val, Pose const &this_pose)
std::string	get (std::string const &key, Pose const &this_pose)
Public Member Functions inherited from core::pose::metrics::PoseMetricCalculator
	PoseMetricCalculator ()
virtual void	notify_energy_change ()

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

Private Attributes
group_set const	groups_
	stores the input - whose neighbors are we finding? More...
core::Real const	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

typedef std::pair< one_group, one_group > protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::group_pair

typedef utility::vector1< group_pair > protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::group_set

typedef std::set< core::Size > protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::one_group

typedef core::pose::metrics::StructureDependentCalculator protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::parent

Constructor & Destructor Documentation

protocols::toolbox::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]
	)

Referenced by clone().

protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::InterGroupNeighborsCalculator

(

InterGroupNeighborsCalculator const &

calculator

)

protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::~InterGroupNeighborsCalculator

(

)

Member Function Documentation

core::pose::metrics::PoseMetricCalculatorOP protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::clone ( ) const

virtual

Implements core::pose::metrics::PoseMetricCalculator.

References InterGroupNeighborsCalculator().

core::Real protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::dist_cutoff ( ) const

inline

return distance cutoff

References dist_cutoff_.

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

inline

return groups

References groups_.

void protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::lookup ( std::string const &  key, basic::MetricValueBase *  valptr  ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References dist_cutoff_, groups_, neighbors_, and num_neighbors_.

std::string protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::print ( std::string const &  key ) const

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References dist_cutoff_, core::sequence::end, groups_, neighbors_, num_neighbors_, and core::id::to_string().

void protocols::toolbox::pose_metric_calculators::InterGroupNeighborsCalculator::recompute ( core::pose::Pose const &  pose )

protectedvirtual

Implements core::pose::metrics::StructureDependentCalculator.

References core::pose::Pose::conformation(), core::graph::Node::const_edge_list_end(), dist_cutoff_, core::sequence::end, core::graph::Edge::get_node(), groups_, neighbors_, num_neighbors_, core::conformation::residue_point_graph_from_conformation(), and core::pose::Pose::total_residue().

Member Data Documentation

core::Real const protocols::toolbox::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 const protocols::toolbox::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::toolbox::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::toolbox::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:

• src/protocols/toolbox/pose_metric_calculators/InterGroupNeighborsCalculator.hh
• src/protocols/toolbox/pose_metric_calculators/InterGroupNeighborsCalculator.cc