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Rosetta 3.4
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Rosetta 3.4
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#include <MMBondAngleEnergy.hh>
Public Types | |
| typedef ContextIndependentTwoBodyEnergy | parent |
Public Member Functions | |
| MMBondAngleEnergy (methods::EnergyMethodOptions const &options) | |
| MMBondAngleEnergy (MMBondAngleEnergy const &src) | |
| ~MMBondAngleEnergy () | |
| 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 | 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 &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) 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 &emap, 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 |
| MMBondAngleEnergy does not have an atomic interation threshold. | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| MMBondAngleEnergy is context independent; indicates that no context graphs are required. | |
| void | residue_type_param_set (core::scoring::mm::MMBondAngleResidueTypeParamSetOP param_set) |
| set underlying MMBondAngleResidueTypeParamSet | |
| core::scoring::mm::MMBondAngleResidueTypeParamSetOP | residue_type_param_set () |
| get underlying MMBondAngleResidueTypeParamSet | |
| core::scoring::mm::MMBondAngleResidueTypeParamSetCOP | residue_type_param_set () const |
| get underlying MMBondAngleResidueTypeParamSet | |
Reimplemented from core::scoring::methods::ContextIndependentTwoBodyEnergy.
| core::scoring::methods::MMBondAngleEnergy::MMBondAngleEnergy | ( | methods::EnergyMethodOptions const & | options | ) |
References core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set().
Referenced by clone().
| core::scoring::methods::MMBondAngleEnergy::MMBondAngleEnergy | ( | MMBondAngleEnergy const & | src | ) |
| core::scoring::methods::MMBondAngleEnergy::~MMBondAngleEnergy | ( | ) |
| Distance core::scoring::methods::MMBondAngleEnergy::atomic_interaction_cutoff | ( | ) | const [virtual] |
MMBondAngleEnergy does not have an atomic interation threshold.
Implements core::scoring::methods::ShortRangeTwoBodyEnergy.
| EnergyMethodOP core::scoring::methods::MMBondAngleEnergy::clone | ( | ) | const [virtual] |
| bool core::scoring::methods::MMBondAngleEnergy::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::MMBondAngleEnergy::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::chemical::ResidueType::atom_type(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::bondangle(), core::chemical::ResidueType::bondangles_for_atom(), core::pose::Pose::conformation(), core::scoring::mm::MMBondAngleScore::dscore(), core::chemical::ResidueType::mm_atom_type_index(), core::scoring::mm_bend, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::chemical::ResidueType::residue_connections_for_atom(), core::pose::Pose::residue_type(), core::chemical::ResidueType::within1bonds_sets_for_atom(), and core::conformation::Residue::xyz().
| void core::scoring::methods::MMBondAngleEnergy::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::conformation::Residue::atom_name(), core::chemical::ResidueType::atom_type(), core::chemical::ResidueType::bondangle(), core::chemical::AtomType::is_virtual(), core::chemical::ResidueType::mm_atom_name(), core::chemical::ResidueType::mm_atom_type_index(), core::scoring::mm_bend, core::chemical::ResidueType::name(), core::chemical::ResidueType::num_bondangles(), core::scoring::mm::MMBondAngleScore::score(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
| void core::scoring::methods::MMBondAngleEnergy::indicate_required_context_graphs | ( | utility::vector1< bool > & | ) | const [virtual] |
MMBondAngleEnergy is context independent; indicates that no context graphs are required.
Implements core::scoring::methods::EnergyMethod.
| void core::scoring::methods::MMBondAngleEnergy::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::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::pose::Pose::conformation(), core::conformation::Residue::connections_to_residue(), core::conformation::Residue::is_bonded(), core::chemical::ResidueType::mm_atom_name(), core::chemical::ResidueType::mm_atom_type_index(), core::scoring::mm_bend, core::chemical::ResidueType::name(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::scoring::mm::MMBondAngleScore::score(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
| core::scoring::mm::MMBondAngleResidueTypeParamSetCOP core::scoring::methods::MMBondAngleEnergy::residue_type_param_set | ( | ) | const [inline] |
get underlying MMBondAngleResidueTypeParamSet
| void core::scoring::methods::MMBondAngleEnergy::residue_type_param_set | ( | core::scoring::mm::MMBondAngleResidueTypeParamSetOP | param_set | ) | [inline] |
set underlying MMBondAngleResidueTypeParamSet
| core::scoring::mm::MMBondAngleResidueTypeParamSetOP core::scoring::methods::MMBondAngleEnergy::residue_type_param_set | ( | ) | [inline] |
get underlying MMBondAngleResidueTypeParamSet
| void core::scoring::methods::MMBondAngleEnergy::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::MMBondAngleEnergy::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::MMBondAngleEnergy::setup_for_scoring | ( | pose::Pose & | pose, |
| ScoreFunction const & | |||
| ) | const [virtual] |
1.7.4
