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Rosetta 3.4
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Rosetta 3.4
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ChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align. More...
#include <ChainbreakEnergy.hh>
Public Types | |
| typedef WholeStructureEnergy | parent |
Public Member Functions | |
| ChainbreakEnergy () | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &, EnergyMap &totals) const |
| called at the end of energy evaluation | |
| 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 core::Size | version () const |
| Return the version of the energy method. | |
ChainbreakEnergy class iterates across all residues in finalize() and determines the penalty between residues i and i+1 by how much their psueduo atoms do not align.
Reimplemented from core::scoring::methods::WholeStructureEnergy.
| core::scoring::methods::ChainbreakEnergy::ChainbreakEnergy | ( | ) |
Referenced by clone().
| virtual EnergyMethodOP core::scoring::methods::ChainbreakEnergy::clone | ( | ) | const [inline, virtual] |
| void core::scoring::methods::ChainbreakEnergy::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::conformation::Residue::atom_name(), core::scoring::chainbreak, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), protocols::kinmatch::xyz(), core::conformation::Atom::xyz(), and core::pose::Pose::xyz().
| void core::scoring::methods::ChainbreakEnergy::finalize_total_energy | ( | pose::Pose & | pose, |
| ScoreFunction const & | , | ||
| EnergyMap & | totals | ||
| ) | const [virtual] |
called at the end of energy evaluation
called at the end of energy evaluation In this case (ChainbreakEnergy), all the calculation is done here
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::chainbreak, core::kinematics::FoldTree::cutpoint(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::residue(), and protocols::kinmatch::xyz().
Referenced by protocols::forge::methods::quadratic_chainbreak().
| void core::scoring::methods::ChainbreakEnergy::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.
| core::Size core::scoring::methods::ChainbreakEnergy::version | ( | ) | const [virtual] |
Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
1.7.4
