an atom-atom neighborlist object More...

#include <NeighborList.hh>

Collaboration diagram for core::scoring::AtomNeighbor:

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.

Definition at line 98 of file NeighborList.hh.

Constructor & Destructor Documentation

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

inline

Definition at line 101 of file NeighborList.hh.

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

Definition at line 103 of file NeighborList.hh.

Member Function Documentation

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

inline

Definition at line 127 of file NeighborList.hh.

References atomno_.

Referenced by core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), and core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 133 of file NeighborList.hh.

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

Definition at line 120 of file NeighborList.hh.

References rsd_.

Referenced by core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative(), core::scoring::methods::MMLJEnergyInter::eval_atom_derivative(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_atom_derivative(), and core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 153 of file NeighborList.hh.

References temp1_.

Referenced by core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 154 of file NeighborList.hh.

References temp2_.

Referenced by core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 155 of file NeighborList.hh.

References temp3_.

Referenced by core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 156 of file NeighborList.hh.

References temp4_.

Referenced by core::scoring::hackelec::HackElecEnergy::finalize_total_energy().

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

inline

Definition at line 140 of file NeighborList.hh.

References weight_.

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

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

inline

fpd

Definition at line 147 of file NeighborList.hh.

References weight_func_.

Member Data Documentation

int core::scoring::AtomNeighbor::atomno_

private

Definition at line 161 of file NeighborList.hh.

Referenced by atomno().

Size core::scoring::AtomNeighbor::path_dist_

private

Definition at line 162 of file NeighborList.hh.

Referenced by path_dist().

int core::scoring::AtomNeighbor::rsd_

private

Definition at line 160 of file NeighborList.hh.

Referenced by rsd().

Real core::scoring::AtomNeighbor::temp1_

mutableprivate

fpd

Definition at line 166 of file NeighborList.hh.

Referenced by temp1().

Real core::scoring::AtomNeighbor::temp2_

mutableprivate

Definition at line 167 of file NeighborList.hh.

Referenced by temp2().

Real core::scoring::AtomNeighbor::temp3_

mutableprivate

Definition at line 168 of file NeighborList.hh.

Referenced by temp3().

Real core::scoring::AtomNeighbor::temp4_

mutableprivate

Definition at line 169 of file NeighborList.hh.

Referenced by temp4().

Real core::scoring::AtomNeighbor::weight_

private

Definition at line 163 of file NeighborList.hh.

Referenced by weight().

Real core::scoring::AtomNeighbor::weight_func_

private

Definition at line 164 of file NeighborList.hh.

Referenced by weight_func().

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

src/core/scoring/NeighborList.hh

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation