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Rosetta 3.4
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Rosetta 3.4
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#include <GaussianOverlapEnergy.hh>
Public Types | |
| typedef ContextIndependentTwoBodyEnergy | parent |
Public Member Functions | |
| GaussianOverlapEnergy () | |
| ~GaussianOverlapEnergy () | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &scorefxn, 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 |
| GaussianOverlapEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now. | |
| Distance | interaction_cutoff () const |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| GaussianOverlapEnergy requires that Energies class maintains a TenANeighborGraph. | |
| 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. | |
Reimplemented from core::scoring::methods::ContextIndependentTwoBodyEnergy.
| core::scoring::methods::GaussianOverlapEnergy::GaussianOverlapEnergy | ( | ) |
Referenced by clone().
| core::scoring::methods::GaussianOverlapEnergy::~GaussianOverlapEnergy | ( | ) |
| Distance core::scoring::methods::GaussianOverlapEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
GaussianOverlapEnergy distance cutoff set to the same cutoff used by EtableEnergy, for now.
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References interaction_cutoff().
| EnergyMethodOP core::scoring::methods::GaussianOverlapEnergy::clone | ( | ) | const [virtual] |
| virtual bool core::scoring::methods::GaussianOverlapEnergy::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::GaussianOverlapEnergy::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.
| void core::scoring::methods::GaussianOverlapEnergy::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::GaussianOverlapEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [virtual] |
GaussianOverlapEnergy requires that Energies class maintains a TenANeighborGraph.
Implements core::scoring::methods::EnergyMethod.
| Distance core::scoring::methods::GaussianOverlapEnergy::interaction_cutoff | ( | ) | const |
non-virtual accessor for speed
non-virtual accessor for speed; assumption: GaussianOverlapEnergy is not inherrited from.
References DIST_TH.
Referenced by atomic_interaction_cutoff().
| void core::scoring::methods::GaussianOverlapEnergy::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.
References core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::chemical::AtomType::lj_radius(), core::conformation::Residue::nheavyatoms(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().
1.7.4
