core::kinematics::tree Namespace Reference

Classes
class	Atom
	Kinematics Atom interface class. More...
class	Atom_
	Kinematics Atom abstract base class. More...
class	BondedAtom
	an atom which are bonded to its parentt, derived from Atom_ More...
class	JumpAtom
	an atom who are connected to its parent via rigid-body transformation "Jump" More...
Typedefs
typedef utility::pointer::access_ptr < Atom >	AtomAP
typedef utility::pointer::owning_ptr < Atom >	AtomOP
Functions
Length	distance (Atom const &atom1, Atom const &atom2)
	Distance between two Atoms.
Length	distance_squared (Atom const &atom1, Atom const &atom2)
	Distance squared between two Atoms.
static basic::Tracer	TR ("core.kinematics.tree.Atom_")
Variables
Jump	BOGUS_JUMP

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Typedef Documentation

typedef utility::pointer::access_ptr< Atom > core::kinematics::tree::AtomAP

typedef utility::pointer::owning_ptr< Atom > core::kinematics::tree::AtomOP

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Function Documentation

Length core::kinematics::tree::distance	(	Atom const &	atom1,
		Atom const &	atom2
	)		[inline]

Distance between two Atoms.

References core::kinematics::tree::Atom::distance().

Length core::kinematics::tree::distance_squared	(	Atom const &	atom1,
		Atom const &	atom2
	)		[inline]

Distance squared between two Atoms.

References core::kinematics::tree::Atom::distance_squared().

Referenced by protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::qsar::scoring_grid::GridBase::diffuse_ring(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), core::scoring::methods::RG_Energy::finalize_total_energy(), protocols::frag_picker::FragmentPicker::fragment_contacts(), core::scoring::electron_density::ElectronDensity::get_nearest_UC(), protocols::ligand_docking::ligand_options::is_interface_vector(), core::pack::min_pack(), core::pack::interaction_graph::RotamerDots::overlaps(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), core::scoring::methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::methods::residues_interact(), and core::kinematics::AtomTree::set_stub_transform().

static basic::Tracer core::kinematics::tree::TR

(

"core.kinematics.tree.Atom_"

)

[static]

Referenced by core::kinematics::tree::Atom_::show().

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Variable Documentation

Jump core::kinematics::tree::BOGUS_JUMP

Referenced by core::kinematics::tree::BondedAtom::jump().