Rosetta 3.4
Public Types | Public Member Functions
core::scoring::methods::MMLJEnergyIntra Class Reference

#include <MMLJEnergyIntra.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 MMLJEnergyIntra ()
 ctor
virtual EnergyMethodOP clone () const
 clone
void setup_for_minimizing (pose::Pose &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map) const
 Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true.
virtual void residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const
 Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
virtual void eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const
 Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative.
virtual bool defines_intrares_energy (EnergyMap const &) const
 Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.
virtual void eval_intrares_energy (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const
 Evaluate the intra-residue energy for a given residue.
virtual Distance atomic_interaction_cutoff () const
 MMLJEnergy does not have an atomic interation threshold.
virtual void indicate_required_context_graphs (utility::vector1< bool > &) const
 MMLJEnergy is context independent; indicates that no context graphs are required.
etable::count_pair::CountPairFunctionCOP get_count_pair_function (Size res1, Size res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 required for neighbor list and to be more lke the ETable
etable::count_pair::CountPairFunctionCOP get_count_pair_function (conformation::Residue const &res1, conformation::Residue const &res2, pose::Pose const &pose, ScoreFunction const &sfxn) const
 required for neighbor list and to be more lke the ETable
etable::count_pair::CountPairFunctionOP get_intrares_countpair (conformation::Residue const &res, pose::Pose const &pose, ScoreFunction const &sfxn) const
 required for neighbor list and to be more lke the ETable

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::MMLJEnergyIntra::MMLJEnergyIntra ( )

ctor

Referenced by clone().


Member Function Documentation

Distance core::scoring::methods::MMLJEnergyIntra::atomic_interaction_cutoff ( ) const [virtual]

MMLJEnergy does not have an atomic interation threshold.

Implements core::scoring::methods::ShortRangeTwoBodyEnergy.

EnergyMethodOP core::scoring::methods::MMLJEnergyIntra::clone ( ) const [virtual]
bool core::scoring::methods::MMLJEnergyIntra::defines_intrares_energy ( EnergyMap const &  weights) const [virtual]

Two body energies are able to define intra-residue energies, and to do so only in the presence of certain non-zero weights. The ScoreFunction will hand over its weight set as it asks whether the energy method defines an intraresidue energy or not.

For example, the Etable method defines intra-residue energies only when one or more of the fa_intra_{atr,rep,sol} weights are non-zero.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::MMLJEnergyIntra::eval_atom_derivative ( id::AtomID const &  id,
pose::Pose const &  pose,
kinematics::DomainMap const &  domain_map,
ScoreFunction const &  sfxn,
EnergyMap const &  emap,
Vector F1,
Vector F2 
) const [virtual]

Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative.

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) "Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations" Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

default implementation does not alter either the F1 or F2 vectors.

Reimplemented from core::scoring::methods::EnergyMethod.

References core::scoring::AtomNeighbor::atomno(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::MM_LJ_INTRA_NBLIST, core::conformation::Atom::mm_type(), core::scoring::AtomNeighbor::path_dist(), core::pose::Pose::residue(), core::scoring::AtomNeighbor::rsd(), core::scoring::Energies::use_nblist(), and core::conformation::Atom::xyz().

void core::scoring::methods::MMLJEnergyIntra::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
etable::count_pair::CountPairFunctionCOP core::scoring::methods::MMLJEnergyIntra::get_count_pair_function ( Size  res1,
Size  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const

required for neighbor list and to be more lke the ETable

References core::pose::Pose::residue().

etable::count_pair::CountPairFunctionCOP core::scoring::methods::MMLJEnergyIntra::get_count_pair_function ( conformation::Residue const &  res1,
conformation::Residue const &  res2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const

required for neighbor list and to be more lke the ETable

References core::scoring::etable::count_pair::CP_CROSSOVER_3.

etable::count_pair::CountPairFunctionOP core::scoring::methods::MMLJEnergyIntra::get_intrares_countpair ( conformation::Residue const &  res,
pose::Pose const &  pose,
ScoreFunction const &  sfxn 
) const

required for neighbor list and to be more lke the ETable

References core::scoring::etable::count_pair::CP_CROSSOVER_3.

void core::scoring::methods::MMLJEnergyIntra::indicate_required_context_graphs ( utility::vector1< bool > &  ) const [virtual]

MMLJEnergy is context independent; indicates that no context graphs are required.

Implements core::scoring::methods::EnergyMethod.

void core::scoring::methods::MMLJEnergyIntra::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]

Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.

Implements core::scoring::methods::TwoBodyEnergy.

void core::scoring::methods::MMLJEnergyIntra::setup_for_minimizing ( pose::Pose ,
ScoreFunction const &  ,
kinematics::MinimizerMapBase const &   
) const [virtual]

Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true.

default implementation noop

Reimplemented from core::scoring::methods::EnergyMethod.

References core::kinematics::MinimizerMapBase::domain_map(), core::pose::Pose::energies(), core::scoring::EnergiesCacheableDataType::MM_LJ_INTRA_NBLIST, core::scoring::mm::MMLJEnergyTable::mm_lj_score(), core::scoring::Energies::use_nblist(), and core::scoring::Energies::use_nblist_auto_update().


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