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Rosetta Core
2014.35
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Rosetta Core
2014.35
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#include <MembraneEnvSmoothEnergy.hh>
Public Types | |
| typedef ContextDependentOneBodyEnergy | parent |
 Public Types inherited from core::scoring::methods::ContextDependentOneBodyEnergy | |
| typedef OneBodyEnergy | parent |
| Public Types inherited from core::scoring::methods::OneBodyEnergy | |
| typedef EnergyMethod | parent |
| Public Types inherited from core::scoring::methods::EnergyMethod | |
| typedef utility::pointer::ReferenceCount | parent |
Public Member Functions | |
| MembraneEnvSmoothEnergy () | |
| virtual EnergyMethodOP | clone () const |
| clone More... | |
| virtual void | setup_for_scoring (pose::Pose &pose, ScoreFunction const &) const |
| computes dScore/dNumNeighbors for all residues for rapid use in later atom derivate calculations More... | |
| virtual void | setup_for_derivatives (pose::Pose &pose, ScoreFunction const &sf) const |
| causes a neighbor graph update More... | |
| virtual void | residue_energy (conformation::Residue const &rsd, pose::Pose const &, EnergyMap &) const |
| evaluates the one-body energy for a residue More... | |
| virtual void | eval_atom_derivative (id::AtomID const &atom_id, pose::Pose const &pose, kinematics::DomainMap const &, ScoreFunction const &, EnergyMap const &weights, Vector &F1, Vector &F2) const |
| increments the F1 and F2 derivative vectors for an atom More... | |
| Distance | atomic_interaction_cutoff () const |
| unused by the MembraneEnvSmoothEnergy class, returns 0 More... | |
| virtual void | indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const |
| Tells the scoring function to maintain the TwelveANeighborGraph. More... | |
| Public Member Functions inherited from core::scoring::methods::ContextDependentOneBodyEnergy | |
| ContextDependentOneBodyEnergy (EnergyMethodCreatorOP) | |
| Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More... | |
| virtual EnergyMethodType | method_type () const |
| Returns the cd_1b element of the EnergyMethodType enumeration; this method should NOT be overridden by derived classes. More... | |
| Public Member Functions inherited from core::scoring::methods::OneBodyEnergy | |
| OneBodyEnergy (EnergyMethodCreatorOP) | |
| Constructor with an EnergyMethodCreator to inform the EnergyMethod parent which ScoreTypes this EnergyMethod is responsible for computing. More... | |
| virtual | ~OneBodyEnergy () |
| virtual bool | defines_score_for_residue (conformation::Residue const &) const |
| During minimization, energy methods are allowed to decide that they say nothing about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for a derivative or an energy. The default behavior is to return "true" for all residues. More... | |
| virtual bool | use_extended_residue_energy_interface () const |
| Rely on the extended version of the residue_energy function during score-function evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData. Return 'true' for the extended version. The default method implemented in this class returns 'false'. More... | |
| virtual void | residue_energy_ext (conformation::Residue const &rsd, ResSingleMinimizationData const &min_data, pose::Pose const &pose, EnergyMap &emap) const |
| Evaluate the one-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 one body energies into the input EnergyMap. 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 setup_for_minimizing_for_residue before this function is invoked. This function should not be called unless the use_extended_residue_energy_interface() method returns "true". Default implementation provided by this base class calls utility::exit(). The Pose merely serves as context, and the input residue is not required to be a member of the Pose. More... | |
| virtual void | setup_for_minimizing_for_residue (conformation::Residue const &rsd, pose::Pose const &, ScoreFunction const &, kinematics::MinimizerMapBase const &, ResSingleMinimizationData &) const |
| Called at the beginning of minimization, allowing this energy method to cache data pertinent for a single residue in the the ResSingleMinimizationData 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. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. 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. More... | |
| virtual bool | requires_a_setup_for_derivatives_for_residue_opportunity (pose::Pose const &pose) const |
| Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation 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_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 void | eval_residue_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 an atom in a residue 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 ResSingleMinimizationData object for the given residue in a call to prepare_for_minimization before this function is invoked. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. DEPRECATED – too slow. More... | |
| virtual bool | defines_dof_derivatives (pose::Pose const &p) 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 Real | eval_residue_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 |
| Evaluate the DOF derivative for a particular residue. The Pose merely serves as context, and the input residue is not required to be a member of the Pose. 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 | finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const |
| called at the end of derivatives evaluation 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 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 | 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 | |
| std::string const & | representative_atom_name (chemical::AA const aa) const |
| returns the atom name for the atom used to represent the sidechain for a particular amino acid; this atom was used to derive the statistics this potential is based on. More... | |
| void | calc_energy (conformation::Residue const &rsd, pose::Pose const &pose, Real const neighbor_count, chemical::AA const aa, Real &score, Real &dscore_dneighbor_count) const |
| convert the neighbor counts for a residue and its aa type into a score and a score derivative. More... | |
| Real | sigmoidish_neighbor (DistanceSquared const sqdist) const |
| given the square distance between a representative atom and a neighbor atom, return the neighborlyness. Ramps from 1 down to 0 over a range. More... | |
| void | increment_f1_f2_for_atom_pair (conformation::Atom const &atom1, conformation::Atom const &atom2, Real weighted_dScore_dN, Vector &F1, Vector &F2) const |
| given a pair of atoms, one of which is a neighbor atom and the other of which is a representative atom, and given the weighted score derivative, increments the F1 and F2 derivatives. More... | |
| virtual core::Size | version () const |
| Return the version of the energy method. More... | |
Private Attributes | |
| utility::vector1< Real > | residue_N_ |
| utility::vector1< Real > | residue_E_ |
| utility::vector1< Real > | residue_dEdN_ |
| ObjexxFCL::FArray3D< Real > | mem_env_log10_ |
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... | |
| core::scoring::methods::MembraneEnvSmoothEnergy::MembraneEnvSmoothEnergy | ( | ) |
References getline(), l, mem_env_log10_, basic::database::open(), tag, and utility_exit_with_message.
Referenced by clone().
| Distance core::scoring::methods::MembraneEnvSmoothEnergy::atomic_interaction_cutoff | ( | ) | const |
unused by the MembraneEnvSmoothEnergy class, returns 0
MembraneEnvSmoothEnergy distance cutoff.
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convert the neighbor counts for a residue and its aa type into a score and a score derivative.
References depth, layer, mem_env_log10_, core::scoring::MembraneEmbed_from_pose(), core::conformation::Residue::seqpos(), and core::conformation::membrane::thickness.
Referenced by residue_energy(), and setup_for_derivatives().
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increments the F1 and F2 derivative vectors for an atom
Special cases handled for when an atom is both the representative atom for an amino acid, and its nbr_atom.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::graph::Edge::get_node(), increment_f1_f2_for_atom_pair(), core::conformation::Residue::is_protein(), core::scoring::Menv_smooth, core::chemical::ResidueType::nbr_atom(), representative_atom_name(), core::pose::Pose::residue(), residue_dEdN_, core::id::AtomID::rsd(), core::conformation::Residue::seqpos(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Residue::type().
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given a pair of atoms, one of which is a neighbor atom and the other of which is a representative atom, and given the weighted score derivative, increments the F1 and F2 derivatives.
References cross(), numeric::xyzVector< class >::distance_squared(), core::scoring::methods::end_sig, core::scoring::methods::end_sig2, core::scoring::methods::start_sig, core::scoring::methods::start_sig2, and core::conformation::Atom::xyz().
Referenced by eval_atom_derivative().
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Tells the scoring function to maintain the TwelveANeighborGraph.
Implements core::scoring::methods::EnergyMethod.
References core::scoring::twelve_A_neighbor_graph.
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returns the atom name for the atom used to represent the sidechain for a particular amino acid; this atom was used to derive the statistics this potential is based on.
returns const & to static data members to avoid expense of string allocation and destruction. Do not call this function on non-canonical aas
References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, core::chemical::aa_val, core::chemical::name_from_aa(), core::chemical::num_canonical_aas, and utility_exit_with_message.
Referenced by eval_atom_derivative(), residue_energy(), and setup_for_derivatives().
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evaluates the one-body energy for a residue
counts the number of nbr atoms within a given radius of the for the input residue. Because the representative atom on the input residue may be in a different location than the representative atom on the same residue when scoring_begin() is called, these neighbor counts cannot be reused; therefore, scoring_begin does not keep neighbor counts.
Implements core::scoring::methods::ContextDependentOneBodyEnergy.
References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), calc_energy(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::energies(), core::conformation::Residue::is_protein(), core::scoring::Menv_smooth, representative_atom_name(), core::pose::Pose::residue(), score, core::conformation::Residue::seqpos(), sigmoidish_neighbor(), core::scoring::Energies::twelveA_neighbor_graph(), and core::conformation::Atom::xyz().
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causes a neighbor graph update
stores dScore/dNumNeighbors so that when neighbor atoms on adjacent residues move, their influence on the score of the surrounding residues is rapidly computed.
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::aa(), core::conformation::Residue::atom_index(), calc_energy(), core::graph::Node::const_edge_list_end(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::energies(), core::graph::Edge::get_node(), nres, representative_atom_name(), core::pose::Pose::residue(), residue_dEdN_, residue_E_, residue_N_, score, sigmoidish_neighbor(), core::pose::Pose::total_residue(), core::pose::Pose::update_residue_neighbors(), and core::conformation::Atom::xyz().
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computes dScore/dNumNeighbors for all residues for rapid use in later atom derivate calculations
Reimplemented from core::scoring::methods::EnergyMethod.
References core::pose::Pose::update_residue_neighbors().
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given the square distance between a representative atom and a neighbor atom, return the neighborlyness. Ramps from 1 down to 0 over a range.
References core::scoring::methods::end_sig, core::scoring::methods::end_sig2, core::scoring::methods::sqr(), core::scoring::methods::start_sig, and core::scoring::methods::start_sig2.
Referenced by residue_energy(), and setup_for_derivatives().
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Return the version of the energy method.
Implements core::scoring::methods::EnergyMethod.
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Referenced by calc_energy(), and MembraneEnvSmoothEnergy().
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Referenced by eval_atom_derivative(), and setup_for_derivatives().
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Referenced by setup_for_derivatives().
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Referenced by setup_for_derivatives().
1.8.7