Rosetta 3.4
Public Member Functions | Protected Member Functions
core::scoring::NeighborList Class Reference

#include <NeighborList.hh>

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List of all members.

Public Member Functions

 NeighborList (kinematics::DomainMap const &domain_map, Real const XX_cutoff, Real const XH_cutoff, Real const HH_cutoff)
virtual ~NeighborList ()
NeighborListOP clone () const
AtomNeighbors const & atom_neighbors (int const pos, int const atomno) const
AtomNeighbors const & atom_neighbors (id::AtomID const &id) const
AtomNeighbors const & upper_atom_neighbors (int const pos, int const atomno) const
AtomNeighbors const & upper_atom_neighbors (id::AtomID const &id) const
AtomNeighbors const & intrares_upper_atom_neighbors (int const pos, int const atomno) const
AtomNeighbors const & intrares_upper_atom_neighbors (id::AtomID const &id) const
template<class T_Etable >
void setup (pose::Pose const &pose, ScoreFunction const &sfxn, T_Etable const &etable_method) const
 Initialize the nblist so that it reflects the current coordinates in the pose.
void check_domain_map (kinematics::DomainMap const &domain_map_in) const
void clear ()
kinematics::DomainMap const & domain_map () const
template<class T_Etable >
void prepare_for_scoring (pose::Pose const &pose, ScoreFunction const &sfxn, T_Etable const &etable_method) const
 If auto_update_, ensure that no atom in the pose has not moved too much since the last time the neighborlist was updated. The neighborlist tracks the starting coords for all atoms, and then updates.
void set_auto_update (Distance move_tolerance)
void disable_auto_update ()

Protected Member Functions

void declare_atoms_neighbors (id::AtomID at1, id::AtomID at2, Size path_dist, Real weight, Real weight_func=1.0) const
void declare_atom_neighbor_1sided (id::AtomID at1, id::AtomID at2, Size path_dist, Real weight, Real weight_func=1.0) const

Constructor & Destructor Documentation

core::scoring::NeighborList::NeighborList ( kinematics::DomainMap const &  domain_map,
Real const  XX_cutoff,
Real const  XH_cutoff,
Real const  HH_cutoff 
)

Referenced by clone().

core::scoring::NeighborList::~NeighborList ( ) [virtual]

References core::scoring::tr().


Member Function Documentation

AtomNeighbors const& core::scoring::NeighborList::atom_neighbors ( int const  pos,
int const  atomno 
) const [inline]
AtomNeighbors const& core::scoring::NeighborList::atom_neighbors ( id::AtomID const &  id) const [inline]
void core::scoring::NeighborList::check_domain_map ( kinematics::DomainMap const &  domain_map_in) const
void core::scoring::NeighborList::clear ( ) [inline]
NeighborListOP core::scoring::NeighborList::clone ( ) const [inline]

References NeighborList().

void core::scoring::NeighborList::declare_atom_neighbor_1sided ( id::AtomID  at1,
id::AtomID  at2,
Size  path_dist,
Real  weight,
Real  weight_func = 1.0 
) const [protected]

Add at2 to atom 1's neighbor lists, but don't touch at2's neighbor lists.

References core::id::AtomID::atomno(), core::id::AtomID::rsd(), and core::scoring::packstat::weight_func().

void core::scoring::NeighborList::declare_atoms_neighbors ( id::AtomID  at1,
id::AtomID  at2,
Size  path_dist,
Real  weight,
Real  weight_func = 1.0 
) const [protected]
void core::scoring::NeighborList::disable_auto_update ( )
kinematics::DomainMap const& core::scoring::NeighborList::domain_map ( ) const [inline]
AtomNeighbors const& core::scoring::NeighborList::intrares_upper_atom_neighbors ( id::AtomID const &  id) const [inline]
AtomNeighbors const& core::scoring::NeighborList::intrares_upper_atom_neighbors ( int const  pos,
int const  atomno 
) const [inline]
template<class T_Etable >
void core::scoring::NeighborList::prepare_for_scoring ( pose::Pose const &  pose,
ScoreFunction const &  sfxn,
T_Etable const &  etable_method 
) const
void core::scoring::NeighborList::set_auto_update ( Distance  move_tolerance)
template<class T_Etable >
void core::scoring::NeighborList::setup ( pose::Pose const &  pose,
ScoreFunction const &  sfxn,
T_Etable const &  etable_method 
) const

Initialize the nblist so that it reflects the current coordinates in the pose.

const so that it may be called within setup_for_scoring T_Etable class must implement the following functions: bool defines_intrares_energy( EnergyMap const & ) const; CountPairFunctionCOP get_intrares_countpair( conformation::Residue const &, pose::Pose const &, ScoreFunction const & ) const; CountPairFunctionCOP get_count_pair_function( Size &, Size &, pose::Pose const &, ScoreFunction const & ) const;

References core::pose::Pose::conformation(), declare_atoms_neighbors(), core::conformation::Conformation::get_residue_mask(), core::conformation::Conformation::get_residue_weight(), core::conformation::Residue::natoms(), core::conformation::Residue::nbr_radius(), core::pose::pose_max_nbr_radius(), core::pose::Pose::residue(), core::conformation::residue_point_graph_from_conformation(), core::pose::Pose::total_residue(), core::scoring::packstat::weight_func(), core::scoring::ScoreFunction::weights(), and core::conformation::Residue::xyz().

Referenced by prepare_for_scoring(), and core::scoring::etable::BaseEtableEnergy< Derived >::setup_for_minimizing().

AtomNeighbors const& core::scoring::NeighborList::upper_atom_neighbors ( int const  pos,
int const  atomno 
) const [inline]
AtomNeighbors const& core::scoring::NeighborList::upper_atom_neighbors ( id::AtomID const &  id) const [inline]

The documentation for this class was generated from the following files:
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