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Rosetta 3.4
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Rosetta 3.4
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#include <Fa_MbsolvEnergy.hh>
Public Types | |
| typedef ContextDependentTwoBodyEnergy | parent |
Public Member Functions | |
| Fa_MbsolvEnergy (etable::Etable const &etable_in, etable::MembEtable const &memb_etable_in) | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &scfxn) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. | |
| virtual void | eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &weights, Vector &F1, Vector &F2) const |
| called during gradient-based minimization inside dfunc | |
| 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 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 &, pose::Pose const &, ScoreFunction const &, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue. | |
| virtual Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? | |
| void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed. | |
| MembraneTopology const & | MembraneTopology_from_pose (pose::Pose const &pose) const |
| Membrane_FAEmbed const & | Membrane_FAEmbed_from_pose (pose::Pose const &pose) const |
| void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &emap) const |
| called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call. | |
Reimplemented from core::scoring::methods::ContextDependentTwoBodyEnergy.
| core::scoring::methods::Fa_MbsolvEnergy::Fa_MbsolvEnergy | ( | etable::Etable const & | etable_in, |
| etable::MembEtable const & | memb_etable_in | ||
| ) |
Referenced by clone().
| Distance core::scoring::methods::Fa_MbsolvEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
how far apart must two heavy atoms be to have a zero interaction energy?
If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References core::scoring::etable::Etable::max_dis().
| EnergyMethodOP core::scoring::methods::Fa_MbsolvEnergy::clone | ( | ) | const [virtual] |
| virtual bool core::scoring::methods::Fa_MbsolvEnergy::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::Fa_MbsolvEnergy::eval_atom_derivative | ( | id::AtomID const & | id, |
| pose::Pose const & | pose, | ||
| kinematics::DomainMap const & | domain_map, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap const & | weights, | ||
| Vector & | F1, | ||
| Vector & | F2 | ||
| ) | const [virtual] |
called during gradient-based minimization inside dfunc
F1 and F2 are not zeroed -- contributions from this atom are just summed in
Reimplemented from core::scoring::methods::EnergyMethod.
References core::conformation::Residue::atom(), core::id::AtomID::atomno(), core::scoring::etable::count_pair::CP_CROSSOVER_3, core::scoring::etable::count_pair::CP_CROSSOVER_4, core::pose::Pose::energies(), core::scoring::Membrane_FAEmbed::fa_proj(), Membrane_FAEmbed_from_pose(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().
| void core::scoring::methods::Fa_MbsolvEnergy::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::scoring::fa_mbsolv.
| void core::scoring::methods::Fa_MbsolvEnergy::finalize_total_energy | ( | pose::Pose & | pose, |
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | total_energy | ||
| ) | const [virtual] |
called by the ScoreFunction at the end of energy evaluation. The derived class has the opportunity to accumulate a score into the pose's total_energy EnergyMap. WholeStructure energies operate within this method; any method using a NeighborList during minimization would also operate within this function call.
called at the end of energy evaluation
Reimplemented from core::scoring::methods::EnergyMethod.
| void core::scoring::methods::Fa_MbsolvEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [virtual] |
Indicate in the context-graphs-required list which context-graphs this energy method requires that the Pose maintain when doing neighbor evaluation. Context graphs are allowed.
Implements core::scoring::methods::EnergyMethod.
| Membrane_FAEmbed const & core::scoring::methods::Fa_MbsolvEnergy::Membrane_FAEmbed_from_pose | ( | pose::Pose const & | pose | ) | const |
Pose must already contain a cenlist object or this method will fail.
References core::pose::Pose::data(), and core::pose::datacache::CacheableDataType::MEMBRANE_FAEMBED.
Referenced by eval_atom_derivative().
| MembraneTopology const & core::scoring::methods::Fa_MbsolvEnergy::MembraneTopology_from_pose | ( | pose::Pose const & | pose | ) | const |
| void core::scoring::methods::Fa_MbsolvEnergy::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::scoring::fa_mbsolv.
| void core::scoring::methods::Fa_MbsolvEnergy::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::scoring::fa_mbsolv, core::pose::Pose::update_residue_neighbors(), and core::scoring::ScoreFunction::weights().
| void core::scoring::methods::Fa_MbsolvEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::Membrane_FAPotential::compute_fa_projection().
1.7.4
