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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< AtomAtomAP
 
typedef utility::pointer::weak_ptr< Atom const > AtomCAP
 
typedef utility::pointer::shared_ptr< AtomAtomOP
 
typedef utility::pointer::shared_ptr< Atom const > AtomCOP
 
typedef utility::pointer::weak_ptr< JumpAtomJumpAtomAP
 
typedef utility::pointer::weak_ptr< JumpAtom const > JumpAtomCAP
 
typedef utility::pointer::shared_ptr< JumpAtomJumpAtomOP
 
typedef utility::pointer::shared_ptr< JumpAtom const > JumpAtomCOP
 
typedef utility::pointer::shared_ptr< BondedAtomBondedAtomOP
 
typedef utility::pointer::shared_ptr< BondedAtom const > BondedAtomCOP
 
typedef utility::pointer::weak_ptr< BondedAtomBondedAtomAP
 
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

◆ AtomAP

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

◆ AtomCAP

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

◆ AtomCOP

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

◆ AtomOP

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

◆ BondedAtomAP

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

◆ BondedAtomCAP

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

◆ BondedAtomCOP

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

◆ BondedAtomOP

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

◆ JumpAtomAP

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

◆ JumpAtomCAP

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

◆ JumpAtomCOP

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

◆ JumpAtomOP

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

Function Documentation

◆ distance()

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

Distance between two Atoms.

◆ distance_squared()

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

Distance squared between two Atoms.

Referenced by core::scoring::lkball::LK_DomeEnergy::accumulate_single_atom_contributions(), core::scoring::motif::align_motif_pose_NCAC_super(), protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(), protocols::matdes::ClashCheckFilter::compute(), protocols::qsar::scoring_grid::SingleGrid::diffuse_ring(), protocols::match::downstream::AtomDistanceSecMatchRPE::evaluate_residues(), protocols::frag_picker::FragmentPicker::fragment_contacts(), protocols::simple_filters::ResidueDepthCalculator::get_exclusion_index(), core::scoring::lkball::LK_DomeEnergy::get_lkd_bridge_fractional_1way(), core::pack::get_residue_current_energy(), 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(), core::pack::interaction_graph::RotamerDots::overlaps(), protocols::vardist_solaccess::VarSolDRotamerDots::overlaps(), core::conformation::Residue::place(), core::scoring::motif::rt6_rt6_bb_dis2_explicit_stupid(), protocols::sic_dock::scores::TrisBpyScore::score_extra(), and core::kinematics::AtomTree::set_stub_transform().

◆ is_collinear()

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

◆ TR() [1/2]

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

◆ TR() [2/2]

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

Variable Documentation

◆ BOGUS_JUMP

Jump core::kinematics::tree::BOGUS_JUMP