protocols::neighbor Namespace Reference

Classes
class	Neighborhood
	A class to determine the neighborhood of a set of residues within a pose. More...

Typedefs
typedef bool(*	NGB_FUN_PTR )(Residue const &r1, Residue const &r2, Pose const &ps)
	type of functions that determine whether two residues are neighbor of one another More...

Functions
static thread_local basic::Tracer	TR ("protocols.neighbor")
bool	in_nrg_graph (Residue const &r1, Residue const &r2, Pose const &ps)
	: returns true iff r2 is a residue whose node in the energy graph is connected to r1's. More...
bool	in_ngbat_sphere (Residue const &r1, Residue const &r2, Pose const &)
	: returns true iff r2's neighbor atom falls within a cutoff distance of r1's neighbor atom. More...

Typedef Documentation

typedef bool(* protocols::neighbor::NGB_FUN_PTR)(Residue const &r1, Residue const &r2, Pose const &ps)

type of functions that determine whether two residues are neighbor of one another

Function Documentation

bool protocols::neighbor::in_ngbat_sphere	(	Residue const &	r1,
		Residue const &	r2,
		Pose const &
	)

: returns true iff r2's neighbor atom falls within a cutoff distance of r1's neighbor atom.

Parameters

[in]	r1	residue r1
[in]	r2	residue r2
[in]	ps	pose to which both residues belong

The squared cutoff distance is specified within the function by constant DCUT2.

References numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::nbr_atom(), and core::conformation::Residue::xyz().

bool protocols::neighbor::in_nrg_graph	(	Residue const &	r1,
		Residue const &	r2,
		Pose const &	ps
	)

: returns true iff r2 is a residue whose node in the energy graph is connected to r1's.

Parameters

[in]	r1	residue r1
[in]	r2	residue r2
[in]	ps	pose to which both residues belong

References core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Edge::get_node(), and core::conformation::Residue::seqpos().

static thread_local basic::Tracer protocols::neighbor::TR ( "protocols.neighbor"  )

static