core::scoring::AtomNeighbor Class Reference

an atom-atom neighborlist object More...

#include <NeighborList.hh>

Public Member Functions
	AtomNeighbor ()
	AtomNeighbor (int const rsd_in, int const atomno_in, Size const path_dist_in, Real const weight_in, Real const weight_func_in=1)
int	rsd () const
int	atomno () const
Size	path_dist () const
Real	weight () const
Real	weight_func () const
	fpd More...
Real &	temp1 () const
Real &	temp2 () const
Real &	temp3 () const
Real &	temp4 () const

Private Attributes
int	rsd_
int	atomno_
Size	path_dist_
Real	weight_
Real	weight_func_
Real	temp1_
	fpd More...
Real	temp2_
Real	temp3_
Real	temp4_

Detailed Description

an atom-atom neighborlist object

The neighborlist is used during minimization to speed atom-atom energy calculations. It stores a list of potentially interacting neighbor atoms for each atom in the system.

The logic for using the nblist is tricky.

Tentative scheme: turn on nblist scoring at start of minimization

at this point, want pose to be fully scored so perhaps a call to scorefxn(pose) ?? Real const start_score( scorefxn( pose ) );

    pose.energies().setup_use_nblist( true );

    Real const start_func( func( vars ) ); // nblist setup inside this call

    now require that all energy evaluations have an identical set of moving
    dofs (guaranteed if all energy calculations are inside function
    evaluations). This is checked inside each scorecaln using the
    nblist.

    when using the nblist, the rsd-rsd neighbor information is not
    updated. This will probably be a good thing in that it will smooth
    the energy landscape during minimization...

    in a nblist score calculation, we do two things: recover cached
    energies for non-pair-moved positions, and get atom-atom energies
    for the pairs that are on the nblist. We don't cache 2d energies
    for moving positions, since we are not looping over rsd nbr links
    for that score calculation so the caching would be pretty time-
    consuming I think.

    The nblist has the count_pair weights stored, so no calls to
    count_pair !!

    turn off nblist scoring at the end of minimization. Since we have not
    been updating rsd-pair energies for moving pairs, and the rsd-rsd
    nblist is potentially out of data, we reset the neighborgraph at this
    point to ensure a complete score calculation next time.

Constructor & Destructor Documentation

core::scoring::AtomNeighbor::AtomNeighbor ( )

inline

core::scoring::AtomNeighbor::AtomNeighbor ( int const  rsd_in, int const  atomno_in, Size const  path_dist_in, Real const  weight_in, Real const  weight_func_in = 1  )

inline

Member Function Documentation

int core::scoring::AtomNeighbor::atomno ( ) const

inline

References atomno_.

Referenced by core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::finalize_total_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::finalize_total_energy(), and core::scoring::elec::FA_ElecEnergy::finalize_total_energy().

Size core::scoring::AtomNeighbor::path_dist ( ) const

inline

References path_dist_.

Referenced by core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), and core::scoring::methods::MMLJEnergyInter::eval_atom_derivative().

int core::scoring::AtomNeighbor::rsd ( ) const

inline

References rsd_.

Referenced by core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::methods::LK_PolarNonPolarEnergy::eval_atom_derivative(), core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), core::scoring::rna::StackElecEnergy::finalize_total_energy(), core::scoring::geometric_solvation::ContextDependentGeometricSolEnergy::finalize_total_energy(), core::scoring::methods::LK_PolarNonPolarEnergy::finalize_total_energy(), and core::scoring::elec::FA_ElecEnergy::finalize_total_energy().

Real& core::scoring::AtomNeighbor::temp1 ( ) const

inline

References temp1_.

Real& core::scoring::AtomNeighbor::temp2 ( ) const

inline

References temp2_.

Real& core::scoring::AtomNeighbor::temp3 ( ) const

inline

References temp3_.

Real& core::scoring::AtomNeighbor::temp4 ( ) const

inline

References temp4_.

Real core::scoring::AtomNeighbor::weight ( ) const

inline

References weight_.

Referenced by core::scoring::elec::FA_ElecEnergy::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), and core::scoring::elec::FA_ElecEnergy::finalize_total_energy().

Real core::scoring::AtomNeighbor::weight_func ( ) const

inline

fpd

References weight_func_.

Member Data Documentation

int core::scoring::AtomNeighbor::atomno_

private

Referenced by atomno().

Size core::scoring::AtomNeighbor::path_dist_

private

Referenced by path_dist().

int core::scoring::AtomNeighbor::rsd_

private

Referenced by rsd().

Real core::scoring::AtomNeighbor::temp1_

mutableprivate

fpd

Referenced by temp1().

Real core::scoring::AtomNeighbor::temp2_

mutableprivate

Referenced by temp2().

Real core::scoring::AtomNeighbor::temp3_

mutableprivate

Referenced by temp3().

Real core::scoring::AtomNeighbor::temp4_

mutableprivate

Referenced by temp4().

Real core::scoring::AtomNeighbor::weight_

private

Referenced by weight().

Real core::scoring::AtomNeighbor::weight_func_

private

Referenced by weight_func().

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

• src/core/scoring/NeighborList.hh