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

#include <DNA_BaseEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 DNA_BaseEnergy ()
virtual EnergyMethodOP clone () const
 clone
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const
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_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const
 Evaluate the intra-residue energy for a given residue.
virtual void eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, 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 Distance atomic_interaction_cutoff () const
 DNA_BaseEnergy distance cutoff.
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 DNA_BaseEnergy.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::DNA_BaseEnergy::DNA_BaseEnergy ( )

Referenced by clone().


Member Function Documentation

Distance core::scoring::methods::DNA_BaseEnergy::atomic_interaction_cutoff ( ) const [virtual]
EnergyMethodOP core::scoring::methods::DNA_BaseEnergy::clone ( ) const [virtual]
virtual bool core::scoring::methods::DNA_BaseEnergy::defines_intrares_energy ( EnergyMap const &  weights) const [inline, 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::DNA_BaseEnergy::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::id::AtomID::atomno(), core::scoring::methods::count_pair_bs(), core::scoring::dna_bp, core::scoring::dna_bs, core::scoring::methods::dna_deriv_atom(), core::scoring::dna::DNA_BasePotential::eval_base_pair_derivative(), core::scoring::dna::DNA_BasePotential::eval_base_step_derivative(), core::pose::Pose::residue(), core::scoring::methods::retrieve_base_partner_from_pose_inline(), core::id::AtomID::rsd(), and core::pose::Pose::total_residue().

virtual void core::scoring::methods::DNA_BaseEnergy::eval_intrares_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [inline, virtual]

Evaluate the intra-residue energy for a given residue.

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

void core::scoring::methods::DNA_BaseEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  context_graphs_required) const [virtual]
void core::scoring::methods::DNA_BaseEnergy::residue_pair_energy ( conformation::Residue const &  rsd1,
conformation::Residue const &  rsd2,
pose::Pose const &  pose,
ScoreFunction const &  sfxn,
EnergyMap emap 
) const [virtual]
void core::scoring::methods::DNA_BaseEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

are these really necessary??????????? move to scheme that doesnt depend on nbr calcn

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

References core::scoring::dna::set_base_partner(), and core::pose::Pose::update_residue_neighbors().

void core::scoring::methods::DNA_BaseEnergy::setup_for_packing ( pose::Pose ,
utility::vector1< bool > const &  ,
utility::vector1< bool > const &   
) const [virtual]
void core::scoring::methods::DNA_BaseEnergy::setup_for_scoring ( pose::Pose pose,
ScoreFunction const &   
) const [virtual]

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