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Rosetta 3.5
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Rosetta 3.5
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#include <CartesianBondedEnergy.hh>
Public Types | |
| typedef ContextIndependentLRTwoBodyEnergy | parent |
 Public Types inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| typedef LongRangeTwoBodyEnergy | parent |
| Public Types inherited from core::scoring::methods::LongRangeTwoBodyEnergy | |
| typedef TwoBodyEnergy | parent |
| Public Types inherited from core::scoring::methods::TwoBodyEnergy | |
| typedef EnergyMethod | parent |
| Public Types inherited from core::scoring::methods::EnergyMethod | |
| typedef utility::pointer::ReferenceCount | parent |
Public Member Functions | |
| CartesianBondedEnergy (methods::EnergyMethodOptions const &options) | |
| EnergyMethod. More... | |
| CartesianBondedEnergy (CartesianBondedEnergy const &src) | |
| ~CartesianBondedEnergy () | |
| virtual EnergyMethodOP | clone () const |
| clone More... | |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| virtual bool | defines_residue_pair_energy (pose::Pose const &pose, Size res1, Size res2) const |
| 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. More... | |
| void | eval_intrares_energy (conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| Evaluate the intra-residue energy for a given residue. More... | |
| void | eval_residue_pair_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &, ResSingleMinimizationData const &, ResPairMinimizationData const &min_data, pose::Pose const &, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%. More... | |
| virtual Real | eval_intraresidue_dof_derivative (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, id::DOF_ID const &dof_id, id::TorsionID const &torsion_id, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights) const |
| 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. More... | |
| virtual bool | defines_intrares_dof_derivatives (pose::Pose const &) const |
| Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive. More... | |
| virtual bool | minimize_in_whole_structure_context (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More... | |
| virtual Distance | atomic_interaction_cutoff () const |
| CartesianBondedEnergy does not have an atomic interation threshold. More... | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &) const |
| CartesianBondedEnergy is context independent; indicates that no context graphs are required. More... | |
| methods::LongRangeEnergyType | long_range_type () const |
| Public Member Functions inherited from core::scoring::methods::ContextIndependentLRTwoBodyEnergy | |
| ContextIndependentLRTwoBodyEnergy (EnergyMethodCreatorOP) | |
| virtual | ~ContextIndependentLRTwoBodyEnergy () |
| EnergyMethodType | method_type () const |
| Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More... | |
| Public Member Functions inherited from core::scoring::methods::LongRangeTwoBodyEnergy | |
| LongRangeTwoBodyEnergy (EnergyMethodCreatorOP creator) | |
| Constructor with an EnergyMethodCreator to inform the grandparent EnergyMethod class which ScoreTypes this EnergyMethod computes. More... | |
| virtual | ~LongRangeTwoBodyEnergy () |
| Public Member Functions inherited from core::scoring::methods::TwoBodyEnergy | |
| TwoBodyEnergy (EnergyMethodCreatorOP) | |
| Constructor, requiring an EnergyMethodCreator. No default constructor provided to force EnergyMethod writers to provide an energy-method-creator at construction time. More... | |
| virtual | ~TwoBodyEnergy () |
| virtual bool | defines_score_for_residue_pair (conformation::Residue const &res1, conformation::Residue const &res2, bool res_moving_wrt_eachother) const |
| During minimization, energy methods are allowed to decide that they say nothing about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default implementation returns "true" for all residue pairs. Context-dependent two-body energies have the option of behaving as if they are context-independent by returning "false" for residue pairs that do no move wrt each other. More... | |
| virtual bool | use_extended_residue_pair_energy_interface () const |
| Rely on the extended version of the residue_pair_energy function during score-function evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which the derived base class has (or should have) cached a piece of data that will make residue-pair energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should return 'true' from this function to use the extended interface. The default method implemented in this class returns 'false'. More... | |
| virtual void | residue_pair_energy_ext (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResPairMinimizationData const &min_data, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the two-body energies for a particular residue, in the context of a given Pose, and with the help of a piece of cached data for minimization, increment those two body energies into the input EnergyMap. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is invoked. This function should not be called unless the use_extended_residue_pair_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). More... | |
| virtual void | setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData &res_data_cache) const |
| Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More... | |
| virtual void | setup_for_minimizing_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &minmap, ResSingleMinimizationData const &res1_data_cache, ResSingleMinimizationData const &res2_data_cache, ResPairMinimizationData &data_cache) const |
| Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResPairMinimizationData that is used for a particular residue in the context of a particular Pose. This base class provides a noop implementation for this function if there is nothing that the derived class needs to perform in this setup phase. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_opportunity (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. More... | |
| virtual void | setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const |
| Do any setup work should the coordinates of this residue (who is still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. This function is used for both intra-residue setup and pre-inter-residue setup. More... | |
| virtual bool | requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
| virtual void | setup_for_derivatives_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, ResSingleMinimizationData &min_data) const |
| Do any setup work necessary before evaluating the derivatives for this residue. More... | |
| virtual bool | requires_a_setup_for_scoring_for_residue_pair_opportunity (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
| virtual void | setup_for_scoring_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const |
| Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically as to possibly require some amount of setup work before scoring should proceed. More... | |
| virtual bool | requires_a_setup_for_derivatives_for_residue_pair_opportunity (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested in doing so. More... | |
| virtual void | setup_for_derivatives_for_residue_pair (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResSingleMinimizationData const &minsingle_data1, ResSingleMinimizationData const &minsingle_data2, pose::Pose const &pose, ScoreFunction const &sfxn, ResPairMinimizationData &data_cache) const |
| Do any setup work necessary before evaluating the derivatives for this residue pair. More... | |
| virtual void | backbone_backbone_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the backbone of rsd1 and the backbone of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the weighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| virtual void | backbone_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the backbone of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| virtual void | sidechain_sidechain_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the interaction between the sidechain of rsd1 and the sidechain of rsd2 and accumulate the unweighted energies. The sum bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must equal the unweighted result of a call to residue_pair_energy. By default, bb_bb & bb_sc return 0 and sc_sc returns residue pair energy. More... | |
| virtual bool | defines_intrares_energy_for_residue (conformation::Residue const &res) const |
| If a score function defines no intra-residue scores for a particular residue, then it may opt-out of being asked during minimization to evaluate the score for this residue. More... | |
| virtual bool | use_extended_intrares_energy_interface () const |
| Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy during minimization routines should return "true" when this function is invoked on them. This class provides a default "return false" implementation so that classes not desiring to take advantage of this alternate interface need to do nothing. More... | |
| virtual void | eval_intrares_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &data_cache, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap &emap) const |
| Evaluate the intra-residue energy for a given residue using the data held within the ResSingleMinimizationData object. This function should be invoked only on derived instances of this class if they return "true" in a call to their use_extended_intrares_energy_interface method. This base class provides a noop implementation for classes that do not implement this interface, or that do not define intrares energies. More... | |
| virtual void | eval_intrares_derivatives (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap const &weights, utility::vector1< DerivVectorPair > &atom_derivs) const |
| Evaluate the derivative for the intra-residue component of this energy method for all the atoms in a residue in the context of a particular pose, and increment the F1 and F2 vectors held in the atom_derivs vector1. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The calling function must also guarantee that there are at least as many entries in the atom_derivs vector1 as there are atoms in the input rsd. More... | |
| virtual void | bump_energy_full (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| virtual void | bump_energy_backbone (conformation::Residue const &, conformation::Residue const &, pose::Pose const &, ScoreFunction const &, EnergyMap &) const |
| virtual void | evaluate_rotamer_intrares_energies (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< core::PackerEnergy > &energies) const |
| Batch computation of rotamer intrares energies. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More... | |
| virtual void | evaluate_rotamer_intrares_energy_maps (conformation::RotamerSetBase const &set, pose::Pose const &pose, ScoreFunction const &sfxn, utility::vector1< EnergyMap > &emaps) const |
| Batch computation of rotamer intrares energy map. Need not be overriden in derived class – by default, iterates over all rotamers, and calls derived class's intrares _energy method. More... | |
| virtual void | evaluate_rotamer_pair_energies (conformation::RotamerSetBase const &set1, conformation::RotamerSetBase const &set2, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, ObjexxFCL::FArray2D< core::PackerEnergy > &energy_table) const |
| Batch computation of rotamer pair energies. Need not be overriden in derived class – by default, iterates over all pairs of rotamers, and calls the derived class's residue_pair_energy method. More... | |
| virtual void | evaluate_rotamer_background_energies (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< core::PackerEnergy > &energy_vector) const |
| Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More... | |
| virtual void | evaluate_rotamer_background_energy_maps (conformation::RotamerSetBase const &set, conformation::Residue const &residue, pose::Pose const &pose, ScoreFunction const &sfxn, EnergyMap const &weights, utility::vector1< EnergyMap > &emaps) const |
| Batch computation of rotamer/background energies. Need not be overriden in derived class – by default, iterates over all rotamers in the set, and calls derived class's residue_pair_energy method for each one against the background rotamr. More... | |
| Public Member Functions inherited from core::scoring::methods::EnergyMethod | |
| EnergyMethod (EnergyMethodCreatorOP creator) | |
| Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More... | |
| EnergyMethod (EnergyMethod const &src) | |
| Copy constructor copies over the score types of the source. More... | |
| virtual | ~EnergyMethod () |
| virtual void | setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const |
| virtual void | prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const |
| virtual void | update_residue_for_packing (pose::Pose &, Size resid) const |
| ensure this function gets called. The default behavior is to do nothing. More... | |
| virtual void | setup_for_minimizing (pose::Pose &, ScoreFunction const &, kinematics::MinimizerMapBase const &) const |
| Called at the beginning of atom tree minimization, this method allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose's Energies object's "use_nblist()" method returns true. More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sfxn) const |
| Called immediately before atom- and DOF-derivatives are calculated allowing the derived class a chance to prepare for future calls. More... | |
| virtual void | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation More... | |
| virtual bool | defines_high_order_terms (pose::Pose const &) const |
| Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More... | |
| 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. More... | |
| virtual void | finalize_total_energy (pose::Pose &pose, ScoreFunction const &sfxn, EnergyMap &total_energy) 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. More... | |
| ScoreTypes const & | score_types () const |
| Returns the score types that this energy method computes. More... | |
Private Member Functions | |
| void | residue_pair_energy_sorted (conformation::Residue const &rsd1, conformation::Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sf, EnergyMap &emap) const |
| Score evaluation methods. More... | |
| void | eval_singleres_energy (conformation::Residue const &rsd, ResidueCartBondedParameters const &rsdparams, Real phi, Real psi, pose::Pose const &pose, EnergyMap &emap) const |
| Methods for intra-residue energies. More... | |
| void | eval_singleres_improper_torsion_energies (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, pose::Pose const &pose, EnergyMap &emap) const |
| helper function to handle intrares improper torsions More... | |
| void | eval_singleres_torsion_energies (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, EnergyMap &emap) const |
| helper function to handle intrares bond torsions More... | |
| void | eval_singleres_angle_energies (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, EnergyMap &emap) const |
| helper function to handle intrares bond angles More... | |
| void | eval_singleres_length_energies (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, pose::Pose const &pose, EnergyMap &emap) const |
| helper function to handle intrares bond lengths More... | |
| void | eval_residue_pair_energies (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, Real phi2, Real psi2, pose::Pose const &pose, EnergyMap &emap) const |
| Methods for inter-residue energies. More... | |
| void | eval_interresidue_angle_energies_two_from_rsd1 (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, pose::Pose const &pose, EnergyMap &emap) const |
| Evaluate all inter. More... | |
| void | eval_interresidue_angle_energies_two_from_rsd2 (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, pose::Pose const &pose, EnergyMap &emap) const |
| void | eval_interresidue_bond_energy (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, pose::Pose const &pose, EnergyMap &emap) const |
| void | eval_improper_torsions (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, pose::Pose const &pose, EnergyMap &emap) const |
| void | eval_singleres_derivatives (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real phi, Real psi, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r_atom_derivs) const |
| Derivative evaluation methods. More... | |
| void | eval_singleres_torsion_derivatives (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r_atom_derivs) const |
| evaluate intra-residue (proper) torsion derivatives More... | |
| void | eval_singleres_angle_derivatives (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r_atom_derivs) const |
| evaluate intra-residue angle derivatives More... | |
| void | eval_singleres_length_derivatives (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, Real const phi, Real const psi, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r_atom_derivs) const |
| evaluate intra-residue bond-length derivatives More... | |
| void | eval_singleres_improper_torsions_derivatives (conformation::Residue const &rsd, ResidueCartBondedParameters const &resparams, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r_atom_derivs) const |
| evaluate intra-residue improper torsion derivatives More... | |
| void | eval_interresidue_angle_derivs_two_from_rsd1 (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi1, Real psi1, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| evaluate inter-residue angle derivatives where two of the atoms defining the angle are from rsd1 More... | |
| void | eval_interresidue_angle_derivs_two_from_rsd2 (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| evaluate inter-residue angle derivatives where two of the atoms defining the angle are from rsd2 More... | |
| void | eval_interresidue_bond_length_derivs (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &rsd1params, ResidueCartBondedParameters const &rsd2params, Real phi2, Real psi2, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| evaluate inter-residue bond-length derivatives More... | |
| void | eval_improper_torsion_derivatives (conformation::Residue const &rsd1, conformation::Residue const &rsd2, ResidueCartBondedParameters const &res1params, ResidueCartBondedParameters const &res2params, EnergyMap const &weights, utility::vector1< DerivVectorPair > &r1_atom_derivs, utility::vector1< DerivVectorPair > &r2_atom_derivs) const |
| evaluate inter-residue improper torsion derivatives More... | |
| Real | eval_score (Real val, Real K, Real val0) const |
| Common to evaluating the score for torsions, angles, and lengths. More... | |
| virtual core::Size | version () const |
| Return the version of the energy method. More... | |
Private Attributes | |
| bool | linear_bonded_potential_ |
Static Private Attributes | |
| static IdealParametersDatabaseOP | db_ =NULL |
| Evaluate the derivative for a More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from core::scoring::methods::EnergyMethod | |
| void | set_score_types (EnergyMethodCreatorOP creator) |
| Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More... | |
the energy method
Definition at line 336 of file CartesianBondedEnergy.hh.
Definition at line 338 of file CartesianBondedEnergy.hh.
| core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy | ( | methods::EnergyMethodOptions const & | options) |
Definition at line 1371 of file CartesianBondedEnergy.cc.
References db_, core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_linear(), core::scoring::methods::EnergyMethodOptions::get_cartesian_bonded_parameters(), and linear_bonded_potential_.
Referenced by clone().
| core::scoring::methods::CartesianBondedEnergy::CartesianBondedEnergy | ( | CartesianBondedEnergy const & | src) |
Definition at line 1387 of file CartesianBondedEnergy.cc.
References linear_bonded_potential_.
| core::scoring::methods::CartesianBondedEnergy::~CartesianBondedEnergy | ( | ) |
Definition at line 1391 of file CartesianBondedEnergy.cc.
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CartesianBondedEnergy does not have an atomic interation threshold.
Definition at line 1818 of file CartesianBondedEnergy.cc.
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clone
Implements core::scoring::methods::EnergyMethod.
Definition at line 1394 of file CartesianBondedEnergy.cc.
References CartesianBondedEnergy().
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Use the dof_derivative interface for this energy method when calculating derivatives? It is possible to define both dof_derivatives and atom-derivatives; they are not mutually exclusive.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
Definition at line 414 of file CartesianBondedEnergy.hh.
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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.
Definition at line 410 of file CartesianBondedEnergy.hh.
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Implements core::scoring::methods::LongRangeTwoBodyEnergy.
Definition at line 1440 of file CartesianBondedEnergy.cc.
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evaluate inter-residue improper torsion derivatives
Definition at line 3068 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::methods::ResidueCartBondedParameters::bb_CA_index(), core::scoring::methods::ResidueCartBondedParameters::bb_H_index(), core::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::methods::ResidueCartBondedParameters::bb_O_index(), core::scoring::methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_torsion_params(), core::scoring::methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_torsion_params(), core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, core::conformation::Residue::is_protein(), linear_bonded_potential_, protocols::swa::phi(), core::conformation::Residue::seqpos(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_derivatives().
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Definition at line 2422 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom_name(), core::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::methods::ResidueCartBondedParameters::bb_CA_index(), core::scoring::methods::ResidueCartBondedParameters::bb_H_index(), core::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::methods::ResidueCartBondedParameters::bb_O_index(), core::scoring::methods::ResidueCartBondedParameters::ca_cprev_n_h_interres_torsion_params(), core::scoring::methods::ResidueCartBondedParameters::ca_nnext_c_o_interres_torsion_params(), core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, CUTOFF, eval_score(), core::conformation::Residue::is_protein(), core::conformation::Residue::name(), core::pose::Pose::pdb_info(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_energies().
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evaluate inter-residue angle derivatives where two of the atoms defining the angle are from rsd1
Definition at line 2747 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::conformation::Residue::connections_to_residue(), db_, core::chemical::ResidueConnection::index(), core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::conformation::Residue::lower_connect(), core::scoring::methods::CartBondedParameters::mu(), core::chemical::num_canonical_aas, core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), core::scoring::methods::ResidueCartBondedParameters::upper_connect_angle_params(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_derivatives().
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evaluate inter-residue angle derivatives where two of the atoms defining the angle are from rsd2
Definition at line 2864 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::chemical::ResidueType::atoms_within_one_bond_of_a_residue_connection(), core::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::conformation::Residue::connections_to_residue(), db_, core::chemical::ResidueConnection::index(), core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::conformation::Residue::lower_connect(), core::scoring::methods::ResidueCartBondedParameters::lower_connect_angle_params(), core::scoring::methods::CartBondedParameters::mu(), core::chemical::num_canonical_aas, core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_derivatives().
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Evaluate all inter.
Definition at line 2102 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, 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::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::conformation::Residue::connections_to_residue(), CUTOFF, db_, eval_score(), core::chemical::ResidueConnection::index(), core::scoring::methods::CartBondedParameters::K(), core::conformation::Residue::lower_connect(), core::scoring::methods::CartBondedParameters::mu(), core::conformation::Residue::name(), core::chemical::num_canonical_aas, core::pose::Pose::pdb_info(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), core::scoring::methods::ResidueCartBondedParameters::upper_connect_angle_params(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_energies().
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Definition at line 2210 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), 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::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::conformation::Residue::connections_to_residue(), CUTOFF, db_, eval_score(), core::chemical::ResidueConnection::index(), core::scoring::methods::CartBondedParameters::K(), core::conformation::Residue::lower_connect(), core::scoring::methods::ResidueCartBondedParameters::lower_connect_angle_params(), core::scoring::methods::CartBondedParameters::mu(), core::conformation::Residue::name(), core::chemical::num_canonical_aas, core::pose::Pose::pdb_info(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_energies().
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Definition at line 2322 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::conformation::Residue::atom(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_length, core::conformation::Residue::connections_to_residue(), core::scoring::methods::ResidueCartBondedParameters::cprev_n_bond_length_params(), CUTOFF, db_, core::kinematics::distance(), eval_score(), core::chemical::ResidueConnection::index(), core::conformation::Residue::lower_connect(), core::conformation::Residue::name(), core::chemical::num_canonical_aas, core::pose::Pose::pdb_info(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_energies().
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evaluate inter-residue bond-length derivatives
Definition at line 2976 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::scoring::methods::ResidueCartBondedParameters::bb_C_index(), core::scoring::methods::ResidueCartBondedParameters::bb_N_index(), core::scoring::cart_bonded, core::scoring::cart_bonded_length, core::conformation::Residue::connections_to_residue(), core::scoring::methods::ResidueCartBondedParameters::cprev_n_bond_length_params(), db_, core::chemical::ResidueConnection::index(), linear_bonded_potential_, core::conformation::Residue::lower_connect(), core::chemical::num_canonical_aas, core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), core::conformation::Residue::seqpos(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect(), and core::conformation::Residue::xyz().
Referenced by eval_residue_pair_derivatives().
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Evaluate the intra-residue energy for a given residue.
Implements core::scoring::methods::TwoBodyEnergy.
Definition at line 1470 of file CartesianBondedEnergy.cc.
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Evaluate dE/dphi and dE/dpsi for the backbone-dependent terms, if they are active.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
Definition at line 1547 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::chemical::ResidueConnection::atomno(), core::id::BB, core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, db_, core::scoring::methods::CartBondedParameters::dK_dphi(), core::scoring::methods::CartBondedParameters::dK_dpsi(), core::scoring::methods::CartBondedParameters::dmu_dphi(), core::scoring::methods::CartBondedParameters::dmu_dpsi(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::chemical::ResidueType::lower_connect(), core::conformation::Residue::mainchain_torsion(), core::scoring::methods::CartBondedParameters::mu(), protocols::swa::phi(), protocols::swa::psi(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::seqpos(), core::id::TorsionID::torsion(), core::pose::Pose::total_residue(), core::id::TorsionID::type(), core::conformation::Residue::type(), core::chemical::ResidueType::upper_connect(), core::id::TorsionID::valid(), core::conformation::Residue::xyz(), and core::pose::Pose::xyz().
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Evaluate the derivative for an atom in rsd1 with respect to rsd2 in the context of a particular pose, and increment the F1 and F2 vectors. This base class provides a default noop implementation of this function. The calling function must guarantee that this EnergyMethod has had the opportunity to update the input ResPairMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. DEPRECATED. Too slow. Too much overhead for each atom; slowed fast-relax runs by ~40%.
Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect to each other and increment the derivatives in atom-derivatives vector1s. The calling function must guarantee that the r1_atom_derivs vector1 holds at least as many entries as there are atoms in rsd1, and that the r2_atom_derivs vector1 holds at least as many entries as there are atoms in rsd2.
Reimplemented from core::scoring::methods::TwoBodyEnergy.
Definition at line 1482 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::chemical::aa_vrt, db_, eval_improper_torsion_derivatives(), eval_interresidue_angle_derivs_two_from_rsd1(), eval_interresidue_angle_derivs_two_from_rsd2(), eval_interresidue_bond_length_derivs(), eval_singleres_derivatives(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_bonded(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::seqpos(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().
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Methods for inter-residue energies.
Evaluate all the inter-residue components
rsd1.seqpos < rsd2.seqpos, and rsd1&rsd2 should be chemically bonded.
Definition at line 2082 of file CartesianBondedEnergy.cc.
References eval_improper_torsions(), eval_interresidue_angle_energies_two_from_rsd1(), eval_interresidue_angle_energies_two_from_rsd2(), and eval_interresidue_bond_energy().
Referenced by residue_pair_energy_sorted().
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Common to evaluating the score for torsions, angles, and lengths.
Evaluate either the harmonic or linearized-harmonic energy given by either: score = 0.5 * K * (val-val0)^2 or score = 0.5 * K * (val-val0)^2 if abs(val-val0) < 1 = 0.5 * K * abs(val-val0) otherwise
Definition at line 3185 of file CartesianBondedEnergy.cc.
References linear_bonded_potential_.
Referenced by eval_improper_torsions(), eval_interresidue_angle_energies_two_from_rsd1(), eval_interresidue_angle_energies_two_from_rsd2(), eval_interresidue_bond_energy(), eval_singleres_angle_energies(), eval_singleres_improper_torsion_energies(), eval_singleres_length_energies(), and eval_singleres_torsion_energies().
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evaluate intra-residue angle derivatives
helper function to handle intrares bond angles
Definition at line 2597 of file CartesianBondedEnergy.cc.
References core::scoring::methods::ResidueCartBondedParameters::angle_parameters(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::methods::CartBondedParameters::is_null(), core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::scoring::methods::CartBondedParameters::mu(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_derivatives().
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helper function to handle intrares bond angles
Definition at line 1998 of file CartesianBondedEnergy.cc.
References core::scoring::methods::ResidueCartBondedParameters::angle_parameters(), core::conformation::Residue::atom_name(), core::scoring::cart_bonded, core::scoring::cart_bonded_angle, CUTOFF, eval_score(), core::scoring::methods::CartBondedParameters::K(), core::scoring::methods::CartBondedParameters::mu(), core::conformation::Residue::name(), core::pose::Pose::pdb_info(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_energy().
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Derivative evaluation methods.
evaluate all intra-residue derivatives
Definition at line 2514 of file CartesianBondedEnergy.cc.
References core::chemical::aa_vrt, eval_singleres_angle_derivatives(), eval_singleres_improper_torsions_derivatives(), eval_singleres_length_derivatives(), eval_singleres_torsion_derivatives(), and core::conformation::Residue::type().
Referenced by eval_residue_pair_derivatives().
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Methods for intra-residue energies.
Definition at line 1884 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, eval_singleres_angle_energies(), eval_singleres_improper_torsion_energies(), eval_singleres_length_energies(), and eval_singleres_torsion_energies().
Referenced by residue_pair_energy_sorted().
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helper function to handle intrares improper torsions
Definition at line 1906 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::atom_name(), core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, CUTOFF, eval_score(), core::scoring::methods::ResidueCartBondedParameters::improper_torsion_parameters(), core::scoring::methods::CartBondedParameters::K(), core::scoring::methods::CartBondedParameters::mu(), core::conformation::Residue::name(), core::pose::Pose::pdb_info(), core::scoring::methods::CartBondedParameters::period(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_energy().
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evaluate intra-residue improper torsion derivatives
Definition at line 2686 of file CartesianBondedEnergy.cc.
References core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, core::scoring::methods::ResidueCartBondedParameters::improper_torsion_parameters(), core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::scoring::methods::CartBondedParameters::mu(), core::scoring::methods::CartBondedParameters::period(), protocols::swa::phi(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_derivatives().
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evaluate intra-residue bond-length derivatives
helper function to handle intrares bond lengths
Definition at line 2643 of file CartesianBondedEnergy.cc.
References core::scoring::cart_bonded, core::scoring::cart_bonded_length, core::scoring::methods::CartBondedParameters::is_null(), core::scoring::methods::CartBondedParameters::K(), core::scoring::methods::ResidueCartBondedParameters::length_parameters(), linear_bonded_potential_, core::scoring::methods::CartBondedParameters::mu(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_derivatives().
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helper function to handle intrares bond lengths
Definition at line 2041 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::atom_name(), core::scoring::cart_bonded, core::scoring::cart_bonded_length, CUTOFF, eval_score(), core::scoring::methods::CartBondedParameters::K(), core::scoring::methods::ResidueCartBondedParameters::length_parameters(), core::scoring::methods::CartBondedParameters::mu(), core::chemical::ResidueType::name(), core::pose::Pose::pdb_info(), core::conformation::Residue::seqpos(), core::scoring::methods::TR(), core::conformation::Residue::type(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_energy().
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evaluate intra-residue (proper) torsion derivatives
helper function to handle intrares bond torsions
Definition at line 2537 of file CartesianBondedEnergy.cc.
References core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, core::scoring::methods::CartBondedParameters::K(), linear_bonded_potential_, core::scoring::methods::CartBondedParameters::mu(), core::scoring::methods::CartBondedParameters::period(), core::scoring::methods::ResidueCartBondedParameters::torsion_parameters(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_derivatives().
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helper function to handle intrares bond torsions
Definition at line 1951 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::atom_name(), core::scoring::cart_bonded, core::scoring::cart_bonded_torsion, CUTOFF, eval_score(), core::scoring::methods::CartBondedParameters::K(), core::scoring::methods::CartBondedParameters::mu(), core::conformation::Residue::name(), core::pose::Pose::pdb_info(), core::scoring::methods::CartBondedParameters::period(), core::conformation::Residue::seqpos(), core::scoring::methods::ResidueCartBondedParameters::torsion_parameters(), core::scoring::methods::TR(), and core::conformation::Residue::xyz().
Referenced by eval_singleres_energy().
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CartesianBondedEnergy is context independent; indicates that no context graphs are required.
Implements core::scoring::methods::EnergyMethod.
Definition at line 1825 of file CartesianBondedEnergy.cc.
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Implements core::scoring::methods::LongRangeTwoBodyEnergy.
Definition at line 1829 of file CartesianBondedEnergy.cc.
References core::scoring::methods::cart_bonded_lr.
Referenced by setup_for_scoring().
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Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin.
Reimplemented from core::scoring::methods::EnergyMethod.
Definition at line 419 of file CartesianBondedEnergy.hh.
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Evaluate the interaction between a given residue pair accumulating the unweighted energies in an EnergyMap.
Implements core::scoring::methods::TwoBodyEnergy.
Definition at line 1452 of file CartesianBondedEnergy.cc.
References residue_pair_energy_sorted(), and core::conformation::Residue::seqpos().
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Score evaluation methods.
here, rsd1.seqpos() < rsd2.seqpos()
Definition at line 1832 of file CartesianBondedEnergy.cc.
References core::conformation::Residue::aa(), core::chemical::aa_pro, core::chemical::aa_vrt, db_, eval_residue_pair_energies(), eval_singleres_energy(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_bonded(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::seqpos(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().
Referenced by residue_pair_energy().
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Reimplemented from core::scoring::methods::EnergyMethod.
Definition at line 1400 of file CartesianBondedEnergy.cc.
References core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::cart_bonded_torsion, core::pose::Pose::energies(), core::pose::symmetry::is_symmetric(), long_range_type(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::scoring::methods::TR().
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Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
Definition at line 3200 of file CartesianBondedEnergy.cc.
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Evaluate the derivative for a
Definition at line 706 of file CartesianBondedEnergy.hh.
Referenced by CartesianBondedEnergy(), eval_interresidue_angle_derivs_two_from_rsd1(), eval_interresidue_angle_derivs_two_from_rsd2(), eval_interresidue_angle_energies_two_from_rsd1(), eval_interresidue_angle_energies_two_from_rsd2(), eval_interresidue_bond_energy(), eval_interresidue_bond_length_derivs(), eval_intraresidue_dof_derivative(), eval_residue_pair_derivatives(), and residue_pair_energy_sorted().
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Definition at line 709 of file CartesianBondedEnergy.hh.
Referenced by CartesianBondedEnergy(), eval_improper_torsion_derivatives(), eval_interresidue_angle_derivs_two_from_rsd1(), eval_interresidue_angle_derivs_two_from_rsd2(), eval_interresidue_bond_length_derivs(), eval_intraresidue_dof_derivative(), eval_score(), eval_singleres_angle_derivatives(), eval_singleres_improper_torsions_derivatives(), eval_singleres_length_derivatives(), and eval_singleres_torsion_derivatives().
1.8.4