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 parent, derived from Atom_ More...
class	JumpAtom
	an atom who are connected to its parent via rigid-body transformation "Jump" More...

Typedefs
typedef utility::pointer::weak_ptr < Atom >	AtomAP
typedef utility::pointer::weak_ptr < Atom const >	AtomCAP
typedef utility::pointer::shared_ptr < Atom >	AtomOP
typedef utility::pointer::shared_ptr < Atom const >	AtomCOP
typedef utility::pointer::weak_ptr < JumpAtom >	JumpAtomAP
typedef utility::pointer::weak_ptr < JumpAtom const >	JumpAtomCAP
typedef utility::pointer::shared_ptr < JumpAtom >	JumpAtomOP
typedef utility::pointer::shared_ptr < JumpAtom const >	JumpAtomCOP
typedef utility::pointer::shared_ptr < BondedAtom >	BondedAtomOP
typedef utility::pointer::shared_ptr < BondedAtom const >	BondedAtomCOP
typedef utility::pointer::weak_ptr < BondedAtom >	BondedAtomAP
typedef utility::pointer::weak_ptr < BondedAtom const >	BondedAtomCAP

Functions
Length	distance (Atom const &atom1, Atom const &atom2)
	Distance between two Atoms. More...
Length	distance_squared (Atom const &atom1, Atom const &atom2)
	Distance squared between two Atoms. More...
bool	is_collinear (Atom const &atom1, Atom const &atom2, Atom const &atom3)
	Check collinearity of three atoms. More...
static basic::Tracer	TR ("core.kinematics.tree.Atom_")
static basic::Tracer	TR ("core.kinematics.tree.BondedAtom")

Variables
Jump	BOGUS_JUMP

Typedef Documentation

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

typedef utility::pointer::weak_ptr< Atom const > core::kinematics::tree::AtomCAP

typedef utility::pointer::shared_ptr< Atom const > core::kinematics::tree::AtomCOP

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

typedef utility::pointer::weak_ptr< BondedAtom > core::kinematics::tree::BondedAtomAP

typedef utility::pointer::weak_ptr< BondedAtom const > core::kinematics::tree::BondedAtomCAP

typedef utility::pointer::shared_ptr< BondedAtom const > core::kinematics::tree::BondedAtomCOP

typedef utility::pointer::shared_ptr< BondedAtom > core::kinematics::tree::BondedAtomOP

typedef utility::pointer::weak_ptr< JumpAtom > core::kinematics::tree::JumpAtomAP

typedef utility::pointer::weak_ptr< JumpAtom const > core::kinematics::tree::JumpAtomCAP

typedef utility::pointer::shared_ptr< JumpAtom const > core::kinematics::tree::JumpAtomCOP

typedef utility::pointer::shared_ptr< JumpAtom > core::kinematics::tree::JumpAtomOP

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 core::select::residue_selector::CloseContactResidueSelector::apply(), core::select::residue_selector::NeighborhoodResidueSelector::apply(), protocols::match::downstream::DownstreamAlgorithm::are_colliding(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), core::scoring::hbonds::HBondEnergy::eval_residue_pair_derivatives(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::frag_picker::FragmentPicker::fragment_contacts(), protocols::simple_filters::ResidueDepthCalculator::get_exclusion_index(), core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_atom_atom_overlap_cache(), core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_atom_atom_overlaps(), core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize_bg_bg_atom_atom_overlaps(), protocols::ligand_docking::ligand_options::is_interface_vector(), core::pack::task::residue_selector::is_sc_bb_clash(), core::pack::task::residue_selector::is_sc_sc_clash(), core::pack::min_pack_optimize(), protocols::vardist_solaccess::VarSolDRotamerDots::overlaps(), core::pack::interaction_graph::RotamerDots::overlaps(), protocols::match::output::UpstreamDownstreamCollisionFilter::passes_hardsphere_filter(), core::energy_methods::PairEnergy::residue_pair_energy(), core::scoring::hbonds::HBondEnergy::residue_pair_energy_ext(), core::scoring::methods::residues_interact(), core::scoring::motif::rt6_rt6_bb_dis2_explicit_stupid(), protocols::sic_dock::scores::TrisBpyScore::score_extra(), core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair(), core::kinematics::AtomTree::set_stub_transform(), and core::scoring::NeighborList::update_from_wide_nblist().

bool core::kinematics::tree::is_collinear ( Atom const &  atom1, Atom const &  atom2, Atom const &  atom3  )

inline

Check collinearity of three atoms.

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

Referenced by core::kinematics::tree::Atom_::input_stub_atom3(), core::kinematics::tree::Atom_::raw_input_stub_atom3(), core::kinematics::tree::BondedAtom::raw_stub_atom3(), and core::kinematics::tree::BondedAtom::stub_atom3().

static basic::Tracer core::kinematics::tree::TR ( "core.kinematics.tree.BondedAtom"  )

static

static basic::Tracer core::kinematics::tree::TR ( "core.kinematics.tree.Atom_"  )

static

Referenced by core::kinematics::tree::Atom_::get_input_stub(), core::kinematics::tree::Atom_::get_stub(), core::kinematics::tree::BondedAtom::keep_dof_fixed(), core::kinematics::tree::Atom_::replace_atom(), and core::kinematics::tree::Atom_::show().

Variable Documentation

Jump core::kinematics::tree::BOGUS_JUMP

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