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

Variable Documentation

Jump core::kinematics::tree::BOGUS_JUMP