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

#include <CustomAtomPairEnergy.hh>

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List of all members.

Public Types

typedef
ContextIndependentTwoBodyEnergy 
parent

Public Member Functions

 CustomAtomPairEnergy (Size const cst_seq_sep)
virtual EnergyMethodOP clone () const
 clone
virtual void setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const
virtual void setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const
virtual void setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const
 Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.
virtual void prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const
virtual void update_residue_for_packing (pose::Pose &, Size resid) const
 ensure this function gets called. The default behavior is to do nothing.
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 &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 Distance atomic_interaction_cutoff () const
 CustomAtomPairEnergy distance cutoff set to be a constant.
Distance interaction_cutoff () const
virtual void indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const
 CustomAtomPairEnergy requires no graphs (yet)
virtual bool defines_intrares_energy (EnergyMap const &) const
 CustomAtomPairEnergy does not define intraresidue interactions.
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.

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::methods::CustomAtomPairEnergy::CustomAtomPairEnergy ( Size const  cst_seq_sep)

Referenced by clone().


Member Function Documentation

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

CustomAtomPairEnergy distance cutoff set to be a constant.

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

References interaction_cutoff().

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

CustomAtomPairEnergy does not define intraresidue interactions.

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

void core::scoring::methods::CustomAtomPairEnergy::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::pose::Pose::conformation(), core::scoring::custom_atom_pair, core::scoring::ScoreFunction::has_zero_weight(), interaction_cutoff(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), and core::conformation::Conformation::xyz().

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

Evaluate the intra-residue energy for a given residue.

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

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

CustomAtomPairEnergy requires no graphs (yet)

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

Distance core::scoring::methods::CustomAtomPairEnergy::interaction_cutoff ( ) const

non-virtual accessor for speed

non-virtual accessor for speed; assumption: CustomAtomPairEnergy is not inherited from.

Referenced by atomic_interaction_cutoff(), eval_atom_derivative(), and residue_pair_energy().

void core::scoring::methods::CustomAtomPairEnergy::prepare_rotamers_for_packing ( pose::Pose const &  ,
conformation::RotamerSetBase  
) const [virtual]

default implementation noop

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

void core::scoring::methods::CustomAtomPairEnergy::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::CustomAtomPairEnergy::setup_for_derivatives ( pose::Pose pose,
ScoreFunction const &  sfxn 
) const [virtual]

Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls.

default implementation noop

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

References core::pose::Pose::update_actcoords(), and core::pose::Pose::update_residue_neighbors().

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

ensure this function gets called. The default behavior is to do nothing.

default implementation noop

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

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


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