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Rosetta 3.4
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Rosetta 3.4
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#include <MMLJEnergyIntra.hh>
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 | |
Reimplemented from core::scoring::methods::ContextIndependentTwoBodyEnergy.
| core::scoring::methods::MMLJEnergyIntra::MMLJEnergyIntra | ( | ) |
ctor
Referenced by clone().
| 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] |
Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
References core::conformation::Residue::atom(), core::scoring::mm_lj_intra_atr, core::scoring::mm_lj_intra_rep, core::chemical::ResidueType::natoms(), and core::conformation::Residue::type().
| 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().
1.7.4
