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Rosetta 3.4
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Rosetta 3.4
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PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment. More...
#include <PeptideBondEnergy.hh>
Public Types | |
| typedef ContextIndependentTwoBodyEnergy | parent |
Public Member Functions | |
| PeptideBondEnergy () | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | residue_pair_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &, EnergyMap &emap) const |
| called at the end of energy evaluation | |
| virtual void | eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| Evaluate the intra-residue energy for a given residue. | |
| 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 | indicate_required_context_graphs (utility::vector1< bool > &) const |
| Chainbreak Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies. | |
| 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 Distance | atomic_interaction_cutoff () const |
| how far apart must two heavy atoms be to have a zero interaction energy? | |
| virtual core::Size | version () const |
| Return the version of the energy method. | |
PeptideBondEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by the distance the C-N bond. Evantually I'd also like to add bond angle constraints as well, but that's handled by OmegaTether at the moment.
Reimplemented from core::scoring::methods::ContextIndependentTwoBodyEnergy.
| core::scoring::methods::PeptideBondEnergy::PeptideBondEnergy | ( | ) |
Referenced by clone().
| Distance core::scoring::methods::PeptideBondEnergy::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.
| virtual EnergyMethodOP core::scoring::methods::PeptideBondEnergy::clone | ( | ) | const [inline, virtual] |
| virtual bool core::scoring::methods::PeptideBondEnergy::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::PeptideBondEnergy::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.
| virtual void core::scoring::methods::PeptideBondEnergy::eval_intrares_energy | ( | conformation::Residue const & | rsd, |
| pose::Pose const & | pose, | ||
| ScoreFunction const & | sfxn, | ||
| EnergyMap & | emap | ||
| ) | const [inline, virtual] |
Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
| void core::scoring::methods::PeptideBondEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const [virtual] |
Chainbreak Energy is context independent and thus indicates that no context graphs need to be maintained by class Energies.
Implements core::scoring::methods::EnergyMethod.
| void core::scoring::methods::PeptideBondEnergy::residue_pair_energy | ( | conformation::Residue const & | rsd1, |
| conformation::Residue const & | rsd2, | ||
| pose::Pose const & | pose, | ||
| ScoreFunction const & | , | ||
| EnergyMap & | emap | ||
| ) | const [virtual] |
called at the end of energy evaluation
called at the end of energy evaluation In this case (PeptideBondEnergy), all the calculation is done here
Implements core::scoring::methods::TwoBodyEnergy.
References core::scoring::constraints::GaussianFunc::func(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::is_bonded(), core::scoring::peptide_bond, core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
| core::Size core::scoring::methods::PeptideBondEnergy::version | ( | ) | const [virtual] |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
1.7.4
