#include <InterGroupNeighborsCalculator.hh>
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) | |
| InterGroupNeighborsCalculator (group_set const &groups, core::Real dist_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::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::pose_metric_calculators::InterGroupNeighborsCalculator::group_pair |
◆ group_set
| typedef utility::vector1< group_pair > protocols::pose_metric_calculators::InterGroupNeighborsCalculator::group_set |
◆ one_group
| typedef std::set< core::Size > protocols::pose_metric_calculators::InterGroupNeighborsCalculator::one_group |
◆ parent
| typedef core::pose::metrics::StructureDependentCalculator protocols::pose_metric_calculators::InterGroupNeighborsCalculator::parent |
Constructor & Destructor Documentation
◆ InterGroupNeighborsCalculator() [1/2]
| protocols::pose_metric_calculators::InterGroupNeighborsCalculator::InterGroupNeighborsCalculator | ( | group_set const & | groups | ) |
◆ InterGroupNeighborsCalculator() [2/2]
| protocols::pose_metric_calculators::InterGroupNeighborsCalculator::InterGroupNeighborsCalculator | ( | group_set const & | groups, |
| core::Real | dist_cutoff | ||
| ) |
References calc_inter_group_, dist_cutoff(), and groups().
Member Function Documentation
◆ clone()
|
overridevirtual |
Implements core::pose::metrics::PoseMetricCalculator.
◆ dist_cutoff()
| core::Real protocols::pose_metric_calculators::InterGroupNeighborsCalculator::dist_cutoff | ( | ) | const |
◆ groups()
| group_set const & protocols::pose_metric_calculators::InterGroupNeighborsCalculator::groups | ( | ) | const |
◆ lookup()
|
overrideprotectedvirtual |
Implements core::pose::metrics::StructureDependentCalculator.
References dist_cutoff_, groups_, neighbors_, and num_neighbors_.
◆ print()
|
overrideprotectedvirtual |
Implements core::pose::metrics::StructureDependentCalculator.
References dist_cutoff_, groups_, neighbors_, num_neighbors_, and core::id::to_string().
◆ recompute()
|
overrideprotectedvirtual |
Implements core::pose::metrics::StructureDependentCalculator.
References calc_inter_group_, dist_cutoff_, groups_, neighbors_, and num_neighbors_.
Member Data Documentation
◆ calc_inter_group_
|
private |
Referenced by InterGroupNeighborsCalculator(), and recompute().
◆ dist_cutoff_
|
private |
stores the input - how far away is a neighbor?
Referenced by dist_cutoff(), lookup(), print(), and recompute().
◆ groups_
|
private |
stores the input - whose neighbors are we finding?
Referenced by groups(), lookup(), print(), and recompute().
◆ neighbors_
|
private |
the set of neighbors to return - union of interfaces between groups
Referenced by lookup(), print(), and recompute().
◆ 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/pose_metric_calculators/InterGroupNeighborsCalculator.hh
- src/protocols/pose_metric_calculators/InterGroupNeighborsCalculator.cc
