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Public Member Functions | Private Member Functions | Private Attributes | Static Private Attributes | List of all members
protocols::constel::NeighTeller Class Reference

#include <NeighTeller.hh>

Public Member Functions

 NeighTeller (core::pose::Pose &ref_pose)
 NeighTeller's constructor. More...
 
bool isneigh (core::conformation::Residue const &tgt, core::conformation::Residue const &prb, core::pose::Pose const &ref_pose)
 : tells whether a probe residue is a neighbor of a target residue. More...
 
bool is_neigh_tree (utility::vector1< core::Size > const &set, core::pose::Pose const &ps)
 : tells whether a set of residues form a tree of neighbors. More...
 

Private Member Functions

void print_nmap (core::Size const nres, std::ostream &os) const
 Prints the neighboring table for a set of residues. More...
 

Private Attributes

core::scoring::ScoreFunctionOP scorefxn
 
core::scoring::methods::EnergyMethodOptions eopts
 
core::scoring::EnergyMap unweighted_emap
 
core::Real fa_atr_weight
 
core::Real const interaction_score_threshold
 
utility::vector1
< utility::vector1< bool > > 
nmap
 

Static Private Attributes

static const int MAXNGB = 10
 : boolean table telling whether two residues in a set are neighbors, for sets of at most MAXNGB residues. More...
 

Constructor & Destructor Documentation

protocols::constel::NeighTeller::NeighTeller ( core::pose::Pose ref_pose)

NeighTeller's constructor.

Parameters
[out]ref_posepose containing the residues whose neighbors are to be identified.
Remarks
For speed, a scorefxn containing only fa_atr is used.

Member Function Documentation

bool protocols::constel::NeighTeller::is_neigh_tree ( utility::vector1< core::Size > const &  set,
core::pose::Pose const &  ps 
)

: tells whether a set of residues form a tree of neighbors.

Parameters
[in]poseindexes of the residues in the set
[in]psthe pose
Returns
true if the set of residues form a tree of neighbors; false otherwise

References core::pose::motif::a(), protocols::match::upstream::b, core::sequence::end, isneigh(), nmap, core::pose::Pose::residue(), and protocols::hybridization::t.

Referenced by protocols::constel::target_constel().

bool protocols::constel::NeighTeller::isneigh ( core::conformation::Residue const &  tgt,
core::conformation::Residue const &  prb,
core::pose::Pose const &  ref_pose 
)

: tells whether a probe residue is a neighbor of a target residue.

Tells whether a probe residue is a neighbor of a target residue.

Parameters
[in]tgtthe target residue.
[in]prbthe probe residue. [in] pose both residues belong to.
Returns
true if prb is a neighbor of tgt; false otherwise.

References core::scoring::EMapVector::clear(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::scoring::eval_scsc_sr2b_energies(), core::scoring::fa_atr, fa_atr_weight, interaction_score_threshold, core::conformation::Residue::is_protein(), scorefxn, and unweighted_emap.

Referenced by is_neigh_tree(), protocols::constel::mk_neigh_list(), protocols::constel::pair_constel_set(), and protocols::constel::triple_constel_set().

void protocols::constel::NeighTeller::print_nmap ( core::Size const  nres,
std::ostream &  os 
) const
private

Prints the neighboring table for a set of residues.

Parameters
[in]nresnumber of residues in the set
[out]outputstream

Line i, column j reports nmap[i][j] (1<=i,j<=nres)

References nmap.

Member Data Documentation

core::scoring::methods::EnergyMethodOptions protocols::constel::NeighTeller::eopts
private
core::Real protocols::constel::NeighTeller::fa_atr_weight
private

Referenced by isneigh().

core::Real const protocols::constel::NeighTeller::interaction_score_threshold
private

Referenced by isneigh().

const int protocols::constel::NeighTeller::MAXNGB = 10
staticprivate

: boolean table telling whether two residues in a set are neighbors, for sets of at most MAXNGB residues.

utility::vector1< utility::vector1<bool> > protocols::constel::NeighTeller::nmap
private

Referenced by is_neigh_tree(), and print_nmap().

core::scoring::ScoreFunctionOP protocols::constel::NeighTeller::scorefxn
private

Referenced by isneigh().

core::scoring::EnergyMap protocols::constel::NeighTeller::unweighted_emap
private

Referenced by isneigh().


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