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_pose

pose 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]	pose	indexes of the residues in the set
[in]	ps	the 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]	tgt	the target residue.
[in]	prb	the 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]	nres	number of residues in the set
[out]	output	stream

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().

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

• src/protocols/constel/NeighTeller.hh
• src/protocols/constel/NeighTeller.cc