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Rosetta 3.4
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Rosetta 3.4
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#include <CustomAtomPairEnergy.hh>
Public Types | |
| typedef ContextIndependentTwoBodyEnergy | parent |
Public Member Functions | |
| CustomAtomPairEnergy (Size const cst_seq_sep) | |
| virtual EnergyMethodOP | clone () const |
| clone | |
| virtual void | setup_for_packing (pose::Pose &pose, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. | |
| virtual void | prepare_rotamers_for_packing (pose::Pose const &pose, conformation::RotamerSetBase &set) const |
| virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
| ensure this function gets called. The default behavior is to do nothing. | |
| 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 &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 |
| CustomAtomPairEnergy distance cutoff set to be a constant. | |
| Distance | interaction_cutoff () const |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| CustomAtomPairEnergy requires no graphs (yet) | |
| virtual bool | defines_intrares_energy (EnergyMap const &) const |
| CustomAtomPairEnergy does not define intraresidue interactions. | |
| 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::CustomAtomPairEnergy::CustomAtomPairEnergy | ( | Size const | cst_seq_sep | ) |
Referenced by clone().
| Distance core::scoring::methods::CustomAtomPairEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
CustomAtomPairEnergy distance cutoff set to be a constant.
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
References interaction_cutoff().
| EnergyMethodOP core::scoring::methods::CustomAtomPairEnergy::clone | ( | ) | const [virtual] |
| bool core::scoring::methods::CustomAtomPairEnergy::defines_intrares_energy | ( | EnergyMap const & | ) | const [virtual] |
CustomAtomPairEnergy does not define intraresidue interactions.
Implements core::scoring::methods::TwoBodyEnergy.
| void core::scoring::methods::CustomAtomPairEnergy::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::id::AtomID::atomno(), core::pose::Pose::conformation(), core::scoring::custom_atom_pair, core::scoring::ScoreFunction::has_zero_weight(), interaction_cutoff(), core::id::AtomID::rsd(), core::pose::Pose::total_residue(), and core::conformation::Conformation::xyz().
| void core::scoring::methods::CustomAtomPairEnergy::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::CustomAtomPairEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | context_graphs_required | ) | const [virtual] |
CustomAtomPairEnergy requires no graphs (yet)
Implements core::scoring::methods::EnergyMethod.
| Distance core::scoring::methods::CustomAtomPairEnergy::interaction_cutoff | ( | ) | const |
non-virtual accessor for speed
non-virtual accessor for speed; assumption: CustomAtomPairEnergy is not inherited from.
Referenced by atomic_interaction_cutoff(), eval_atom_derivative(), and residue_pair_energy().
| void core::scoring::methods::CustomAtomPairEnergy::prepare_rotamers_for_packing | ( | pose::Pose const & | , |
| conformation::RotamerSetBase & | |||
| ) | const [virtual] |
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
| void core::scoring::methods::CustomAtomPairEnergy::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::custom_atom_pair, core::chemical::ResidueType::has(), core::scoring::ScoreFunction::has_zero_weight(), interaction_cutoff(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
| void core::scoring::methods::CustomAtomPairEnergy::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::pose::Pose::update_actcoords(), and core::pose::Pose::update_residue_neighbors().
| void core::scoring::methods::CustomAtomPairEnergy::setup_for_packing | ( | pose::Pose & | , |
| utility::vector1< bool > const & | , | ||
| utility::vector1< bool > const & | |||
| ) | const [virtual] |
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_actcoords(), and core::pose::Pose::update_residue_neighbors().
| void core::scoring::methods::CustomAtomPairEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
Reimplemented from core::scoring::methods::EnergyMethod.
References core::scoring::custom_atom_pair, core::pose::get_comment(), core::scoring::constraints::SOGFunc_Impl::read_data(), core::pose::Pose::total_residue(), core::scoring::methods::tr(), core::pose::Pose::update_actcoords(), and core::pose::Pose::update_residue_neighbors().
| void core::scoring::methods::CustomAtomPairEnergy::update_residue_for_packing | ( | pose::Pose & | , |
| Size | resid | ||
| ) | const [virtual] |
ensure this function gets called. The default behavior is to do nothing.
default implementation noop
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_actcoord().
1.7.4
