Rosetta 3.4
Public Types | Public Member Functions
core::scoring::rna::RNA_FullAtomVDW_BasePhosphate Class Reference

#include <RNA_FullAtomVDW_BasePhosphate.hh>

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List of all members.

Public Types

typedef
core::scoring::methods::ContextIndependentOneBodyEnergy 
parent

Public Member Functions

 RNA_FullAtomVDW_BasePhosphate (etable::EtableEnergy const &etable_energy_in, etable::Etable const &etable_in)
 ctor
virtual ~RNA_FullAtomVDW_BasePhosphate ()
 dtor
virtual
core::scoring::methods::EnergyMethodOP 
clone () const
 clone
void residue_fast_pair_energy_attached_H (core::conformation::Residue const &res1, int const atomno1, core::conformation::Residue const &res2, Size const atomno2, Size const at1hbegin, Size const at1hend, Size const at2hbegin, Size const at2hend, EnergyMap &emap) const
virtual void residue_energy (conformation::Residue const &rsd, EnergyMap &emap) const
virtual void residue_energy (conformation::Residue const &rsd, pose::Pose const &, EnergyMap &emap) const
 Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).
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 void setup_for_scoring (pose::Pose &pose, scoring::ScoreFunction const &) const
virtual void setup_for_derivatives (pose::Pose &pose, scoring::ScoreFunction const &) const

Member Typedef Documentation


Constructor & Destructor Documentation

core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::RNA_FullAtomVDW_BasePhosphate ( etable::EtableEnergy const &  etable_energy_in,
etable::Etable const &  etable_in 
)

ctor

constructor

Referenced by clone().

core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::~RNA_FullAtomVDW_BasePhosphate ( ) [virtual]

dtor


Member Function Documentation

methods::EnergyMethodOP core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::clone ( ) const [virtual]
void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::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::conformation::Residue::atom(), core::chemical::rna::RNA_ResidueType::atom_is_phosphate(), core::scoring::etable::BaseEtableEnergy< Derived >::eval_dE_dR_over_r(), core::scoring::fa_intra_RNA_base_phos_sol, core::conformation::Residue::is_RNA(), core::chemical::rna::RNA_ResidueType::is_RNA_base_atom(), core::conformation::Residue::is_virtual(), core::conformation::Residue::natoms(), core::conformation::Residue::path_distance(), core::pose::Pose::residue(), and core::conformation::Residue::RNA_type().

void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy ( conformation::Residue const &  rsd,
pose::Pose const &  pose,
EnergyMap emap 
) const [virtual]

Evaluate the one-body energies for a particular residue, in the context of a given Pose, and increment those energies in the input Emap (do not overwrite them).

Implements core::scoring::methods::ContextIndependentOneBodyEnergy.

References residue_energy().

void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_energy ( conformation::Residue const &  rsd,
EnergyMap emap 
) const [virtual]
void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::residue_fast_pair_energy_attached_H ( core::conformation::Residue const &  res1,
int const  atomno1,
core::conformation::Residue const &  res2,
Size const  atomno2,
Size const  at1hbegin,
Size const  at1hend,
Size const  at2hbegin,
Size const  at2hend,
EnergyMap emap 
) const
void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_derivatives ( pose::Pose pose,
scoring::ScoreFunction const &   
) const [virtual]
void core::scoring::rna::RNA_FullAtomVDW_BasePhosphate::setup_for_scoring ( pose::Pose pose,
scoring::ScoreFunction const &   
) const [virtual]

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